Thu Oct 8 02:57:43 UTC 2020 I: starting to build libsmithwaterman/buster/armhf on jenkins on '2020-10-08 02:57' Thu Oct 8 02:57:43 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/1101/console.log Thu Oct 8 02:57:43 UTC 2020 I: Downloading source for buster/libsmithwaterman=0.0+git20160702.2610e25-7 --2020-10-08 02:57:43-- http://deb.debian.org/debian/pool/main/libs/libsmithwaterman/libsmithwaterman_0.0+git20160702.2610e25-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2280 (2.2K) Saving to: ‘libsmithwaterman_0.0+git20160702.2610e25-7.dsc’ 0K .. 100% 1.54M=0.001s 2020-10-08 02:57:43 (1.54 MB/s) - ‘libsmithwaterman_0.0+git20160702.2610e25-7.dsc’ saved [2280/2280] Thu Oct 8 02:57:43 UTC 2020 I: libsmithwaterman_0.0+git20160702.2610e25-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libsmithwaterman Binary: libsmithwaterman0, libsmithwaterman-dev, smithwaterman Architecture: any Version: 0.0+git20160702.2610e25-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/ekg/smithwaterman Standards-Version: 4.2.0 Vcs-Browser: https://salsa.debian.org/med-team/libsmithwaterman Vcs-Git: https://salsa.debian.org/med-team/libsmithwaterman.git Build-Depends: debhelper (>= 11~), d-shlibs, libdisorder-dev Package-List: libsmithwaterman-dev deb libdevel optional arch=any libsmithwaterman0 deb libs optional arch=any smithwaterman deb science optional arch=any Checksums-Sha1: 6b131fcd61fdcbd2d86ac7ea415983caf3a0e03e 24856 libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz 3343a815738b89ec4208d8d01644da545488e78e 6292 libsmithwaterman_0.0+git20160702.2610e25-7.debian.tar.xz Checksums-Sha256: 6266f043c8a12cad8b1309f620c180fc422a1e9ee9df0163691652fa523f5bd3 24856 libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz 0e00744a30307caa172a479bab5dc88dd91a6708bd4bd95c35aaa96fbc2d15e8 6292 libsmithwaterman_0.0+git20160702.2610e25-7.debian.tar.xz Files: 75f2ad1f67ed481fcd8b8a4178950e5c 24856 libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz a56ad970987c74b7bd285022b0db368f 6292 libsmithwaterman_0.0+git20160702.2610e25-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAltxabYACgkQr8/sjmac 4cJDiA//ShEA8xjg7/D89tGVXcJPLKGaqWTX1z81hE5QM6JkLUKUMFK9cGe5AhwM P12IZsq8YhriZJe6OnIVaOuKyfGrShWksnOlNp1ZGIGGVca4rd/SuIYHs55K5PBp ZgEDmtyZbqepPJiAf0o9QLrFSw7dIltzfQ9jtGJ0mSTsHQvZL3384RFyEDVjXWUK VCR8al8+nrhmVR9/b7eDVz73yg+G0WFWTKDWolB6LtNNEpL1vBf5vbaREUefnSje 6F0w0IL46ap7CrYUMrj3j562s3JniwJkkzFSdntt8B/lNnnK3bPm8dL+4uEfYuR5 6GCDYAfQEf2DJY6YReF8npZV90l2RrgR3Ag/6JhTHDeMCT4tCc4uerWYSc96UJnW lvgTFHOwTFPdfknQKSz3LKuP8CupJxcvZYWMbeyQfRgbtVk+w7Aa9kYVsZqzSa0p xf8YsugbcuZj2QTaBASCBS/9pqU3QUQ2+jD7e3Yk2QEVSr9HQEbCpuk6yCleeFM/ xYoIvpmr2aBPQMXXJrq0IOxdSzCSUktBfRYoP3G28bHTEIv8WTu39XWP+cJupTXw gEhkGgdOzJKUkgpXnVuEglZzqUG5gsykGxZ1EBXPFWTnh23zQWDs3CuVLJQ1YueW rSEbYJCxsGGhMEmtLXREcNMOsP2JzAQKCWkZAT4TJYLY+Zm2/fE= =qfiF -----END PGP SIGNATURE----- Thu Oct 8 02:57:43 UTC 2020 I: Checking whether the package is not for us Thu Oct 8 02:57:43 UTC 2020 I: Starting 1st build on remote node cbxi4pro0-armhf-rb.debian.net. Thu Oct 8 02:57:43 UTC 2020 I: Preparing to do remote build '1' on cbxi4pro0-armhf-rb.debian.net. Thu Oct 8 03:02:43 UTC 2020 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 7 14:57:51 -12 2020 I: pbuilder-time-stamp: 1602125871 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [libsmithwaterman_0.0+git20160702.2610e25-7.dsc] I: copying [./libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz] I: copying [./libsmithwaterman_0.0+git20160702.2610e25-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Aug 12 23:21:26 2018 -12 gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libsmithwaterman_0.0+git20160702.2610e25-7.dsc dpkg-source: info: extracting libsmithwaterman in libsmithwaterman-0.0+git20160702.2610e25 dpkg-source: info: unpacking libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz dpkg-source: info: unpacking libsmithwaterman_0.0+git20160702.2610e25-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying autoconf.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/22571/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 parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='51f87120c8a144bfbce84d60854783ba' 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='22571' 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.yUgYwbppuB/pbuilderrc_NWxY --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/b1 --logfile b1/build.log libsmithwaterman_0.0+git20160702.2610e25-7.dsc' SUDO_GID='115' SUDO_UID='111' 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 cbxi4pro0 4.19.0-11-armmp #1 SMP Debian 4.19.146-1 (2020-09-17) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 6 20:26 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/22571/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 (>= 11~), d-shlibs, libdisorder-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 ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libdisorder-dev; however: Package libdisorder-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} bsdmainutils{a} d-shlibs{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} libbsd0{a} libcroco3{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 18.2 MB of archives. After unpacking 63.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf d-shlibs all 0.84 [17.2 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 25 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-1 [4540 B] Get: 36 http://deb.debian.org/debian buster/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-1 [4092 B] Fetched 18.2 MB in 2s (10.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../17-d-shlibs_0.84_all.deb ... Unpacking d-shlibs (0.84) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../25-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../26-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../28-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../29-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-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 .../32-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libdisorder0:armhf. Preparing to unpack .../34-libdisorder0_0.0.2+git20130809.8062ee1-1_armhf.deb ... Unpacking libdisorder0:armhf (0.0.2+git20130809.8062ee1-1) ... Selecting previously unselected package libdisorder-dev:armhf. Preparing to unpack .../35-libdisorder-dev_0.0.2+git20130809.8062ee1-1_armhf.deb ... Unpacking libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up d-shlibs (0.84) ... Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/libsmithwaterman-0.0+git20160702.2610e25/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package libsmithwaterman dpkg-buildpackage: info: source version 0.0+git20160702.2610e25-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Graham Inggs dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules build dh build --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel aclocal: warning: couldn't open directory 'config': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' libtoolize: Consider adding '-I config' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:30: installing 'config/compile' configure.ac:30: installing 'config/config.guess' configure.ac:30: installing 'config/config.sub' configure.ac:18: installing 'config/install-sh' configure.ac:18: installing 'config/missing' Makefile.am: installing 'config/depcomp' dh_auto_configure -O--no-parallel ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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 whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate ./configure: line 11509: AX_CXXFLAGS: command not found checking for ANSI C header files... (cached) yes checking for stdlib.h... (cached) yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libsmithwaterman.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' make all-am make[2]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smithwaterman.o smithwaterman.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsmithwaterman_la-BandedSmithWaterman.lo `test -f 'BandedSmithWaterman.cpp' || echo './'`BandedSmithWaterman.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c BandedSmithWaterman.cpp -fPIC -DPIC -o .libs/libsmithwaterman_la-BandedSmithWaterman.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c BandedSmithWaterman.cpp -o libsmithwaterman_la-BandedSmithWaterman.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsmithwaterman_la-IndelAllele.lo `test -f 'IndelAllele.cpp' || echo './'`IndelAllele.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c IndelAllele.cpp -fPIC -DPIC -o .libs/libsmithwaterman_la-IndelAllele.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c IndelAllele.cpp -o libsmithwaterman_la-IndelAllele.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsmithwaterman_la-LeftAlign.lo `test -f 'LeftAlign.cpp' || echo './'`LeftAlign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c LeftAlign.cpp -fPIC -DPIC -o .libs/libsmithwaterman_la-LeftAlign.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c LeftAlign.cpp -o libsmithwaterman_la-LeftAlign.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsmithwaterman_la-Repeats.lo `test -f 'Repeats.cpp' || echo './'`Repeats.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c Repeats.cpp -fPIC -DPIC -o .libs/libsmithwaterman_la-Repeats.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c Repeats.cpp -o libsmithwaterman_la-Repeats.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsmithwaterman_la-SmithWatermanGotoh.lo `test -f 'SmithWatermanGotoh.cpp' || echo './'`SmithWatermanGotoh.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c SmithWatermanGotoh.cpp -fPIC -DPIC -o .libs/libsmithwaterman_la-SmithWatermanGotoh.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -c SmithWatermanGotoh.cpp -o libsmithwaterman_la-SmithWatermanGotoh.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0 -Wl,-z,relro -Wl,-z,now -o libsmithwaterman.la -rpath /usr/lib/arm-linux-gnueabihf libsmithwaterman_la-BandedSmithWaterman.lo libsmithwaterman_la-IndelAllele.lo libsmithwaterman_la-LeftAlign.lo libsmithwaterman_la-Repeats.lo libsmithwaterman_la-SmithWatermanGotoh.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/8/crtbeginS.o .libs/libsmithwaterman_la-BandedSmithWaterman.o .libs/libsmithwaterman_la-IndelAllele.o .libs/libsmithwaterman_la-LeftAlign.o .libs/libsmithwaterman_la-Repeats.o .libs/libsmithwaterman_la-SmithWatermanGotoh.o -L/usr/lib/gcc/arm-linux-gnueabihf/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/8/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsmithwaterman.so.0 -o .libs/libsmithwaterman.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsmithwaterman.so.0" && ln -s "libsmithwaterman.so.0.0.0" "libsmithwaterman.so.0") libtool: link: (cd ".libs" && rm -f "libsmithwaterman.so" && ln -s "libsmithwaterman.so.0.0.0" "libsmithwaterman.so") libtool: link: ar cru .libs/libsmithwaterman.a libsmithwaterman_la-BandedSmithWaterman.o libsmithwaterman_la-IndelAllele.o libsmithwaterman_la-LeftAlign.o libsmithwaterman_la-Repeats.o libsmithwaterman_la-SmithWatermanGotoh.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libsmithwaterman.a libtool: link: ( cd ".libs" && rm -f "libsmithwaterman.la" && ln -s "../libsmithwaterman.la" "libsmithwaterman.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smithwaterman smithwaterman.o libsmithwaterman.la -ldisorder libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libsmithwaterman-0.0+git20160702.2610e25=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/smithwaterman smithwaterman.o ./.libs/libsmithwaterman.so -ldisorder make[2]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' make[1]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' dh_auto_test -O--no-parallel make -j1 check VERBOSE=1 make[1]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' make[1]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --no-parallel dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/build/libsmithwaterman-0.0\+git20160702.2610e25/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' make[2]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' /bin/mkdir -p '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ./libtool --mode=install /usr/bin/install -c libsmithwaterman.la '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libsmithwaterman.so.0.0.0 /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so.0.0.0 libtool: install: (cd /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsmithwaterman.so.0.0.0 libsmithwaterman.so.0 || { rm -f libsmithwaterman.so.0 && ln -s libsmithwaterman.so.0.0.0 libsmithwaterman.so.0; }; }) libtool: install: (cd /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsmithwaterman.so.0.0.0 libsmithwaterman.so || { rm -f libsmithwaterman.so && ln -s libsmithwaterman.so.0.0.0 libsmithwaterman.so; }; }) libtool: install: /usr/bin/install -c .libs/libsmithwaterman.lai /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.la libtool: install: /usr/bin/install -c .libs/libsmithwaterman.a /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.a libtool: install: chmod 644 /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.a libtool: install: ranlib /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c smithwaterman '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/bin' libtool: warning: 'libsmithwaterman.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/smithwaterman /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/bin/smithwaterman /bin/mkdir -p '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/include/smithwaterman' /usr/bin/install -c -m 644 BandedSmithWaterman.h IndelAllele.h LeftAlign.h Mosaik.h Repeats.h SmithWatermanGotoh.h convert.h '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/include/smithwaterman' /bin/mkdir -p '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 libsmithwaterman.pc '/build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[2]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' make[1]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' debian/rules override_dh_install make[1]: Entering directory '/build/libsmithwaterman-0.0+git20160702.2610e25' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libsmithwaterman-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libsmithwaterman0/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.a debian/libsmithwaterman-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so debian/libsmithwaterman-dev/usr/lib/arm-linux-gnueabihf mv /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so.0 debian/libsmithwaterman0/usr/lib/arm-linux-gnueabihf mv /build/libsmithwaterman-0.0+git20160702.2610e25/debian/tmp/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so.0.0.0 debian/libsmithwaterman0/usr/lib/arm-linux-gnueabihf PKGDEV=libsmithwaterman-dev PKGSHL=libsmithwaterman0 install -d -m 755 debian/libsmithwaterman-dev/usr/include mv debian/tmp/usr/include/smithwaterman debian/libsmithwaterman-dev/usr/include install -d -m 755 debian/libsmithwaterman-dev/usr/lib/arm-linux-gnueabihf/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libsmithwaterman-dev/usr/lib/arm-linux-gnueabihf/pkgconfig make[1]: Leaving directory '/build/libsmithwaterman-0.0+git20160702.2610e25' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installinit -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_strip -O--no-parallel dh_makeshlibs -O--no-parallel dpkg-gensymbols: warning: debian/libsmithwaterman0/DEBIAN/symbols doesn't match completely debian/libsmithwaterman0.symbols --- debian/libsmithwaterman0.symbols (libsmithwaterman0_0.0+git20160702.2610e25-7_armhf) +++ dpkg-gensymbolsz3xgEF 2020-10-07 15:02:15.462095789 -1200 @@ -72,9 +72,9 @@ (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE12_M_erase_auxESt23_Rb_tree_const_iteratorIS8_E@Base 0.0+git20160702.2610e25 (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_@Base 0.0+git20160702.2610e25 _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_@Base 0.0+git20160702.2610e25 - (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base 0.0+git20160702.2610e25 +#MISSING: 0.0+git20160702.2610e25-7# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base 0.0+git20160702.2610e25 _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E@Base 0.0+git20160702.2610e25 - (optional)_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_@Base 0.0+git20160702.2610e25 +#MISSING: 0.0+git20160702.2610e25-7# (optional)_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_@Base 0.0+git20160702.2610e25 _ZeqRK11IndelAlleleS1_@Base 0.0+git20160702.2610e25 _ZlsRSoRK11IndelAllele@Base 0.0+git20160702.2610e25 _ZltRK11IndelAlleleS1_@Base 0.0+git20160702.2610e25 dh_shlibdeps -O--no-parallel dpkg-shlibdeps: warning: symbol shannon_H used by debian/libsmithwaterman0/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so.0.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libsmithwaterman0/usr/lib/arm-linux-gnueabihf/libsmithwaterman.so.0.0.0 found in none of the libraries dpkg-shlibdeps: warning: debian/smithwaterman/usr/bin/smithwaterman contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/smithwaterman/usr/bin/smithwaterman was not linked against libdisorder.so.0 (it uses none of the library's symbols) dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dpkg-gencontrol: warning: Depends field of package libsmithwaterman-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'libsmithwaterman0' in '../libsmithwaterman0_0.0+git20160702.2610e25-7_armhf.deb'. dpkg-deb: building package 'smithwaterman-dbgsym' in '../smithwaterman-dbgsym_0.0+git20160702.2610e25-7_armhf.deb'. dpkg-deb: building package 'libsmithwaterman-dev' in '../libsmithwaterman-dev_0.0+git20160702.2610e25-7_armhf.deb'. dpkg-deb: building package 'libsmithwaterman0-dbgsym' in '../libsmithwaterman0-dbgsym_0.0+git20160702.2610e25-7_armhf.deb'. dpkg-deb: building package 'smithwaterman' in '../smithwaterman_0.0+git20160702.2610e25-7_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libsmithwaterman_0.0+git20160702.2610e25-7_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) 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/22571 and its subdirectories I: Current time: Wed Oct 7 15:02:38 -12 2020 I: pbuilder-time-stamp: 1602126158 Thu Oct 8 03:02:45 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Thu Oct 8 03:02:45 UTC 2020 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Thu Oct 8 03:05:02 UTC 2020 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Thu Oct 8 03:05:04 UTC 2020 I: libsmithwaterman_0.0+git20160702.2610e25-7_armhf.changes: Format: 1.8 Date: Mon, 13 Aug 2018 11:16:53 +0000 Source: libsmithwaterman Binary: libsmithwaterman-dev libsmithwaterman0 libsmithwaterman0-dbgsym smithwaterman smithwaterman-dbgsym Architecture: armhf Version: 0.0+git20160702.2610e25-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Graham Inggs Description: libsmithwaterman-dev - determine similar regions between two strings or genomic sequence libsmithwaterman0 - determine similar regions between two strings or genomic sequence smithwaterman - determine similar regions between two strings or genomic sequence Changes: libsmithwaterman (0.0+git20160702.2610e25-7) unstable; urgency=medium . * Team upload * Mark specific symbols for mips and mipsel as optional Checksums-Sha1: fda28ee4a84fd349b401bfd4de2758ff0807b9f0 36088 libsmithwaterman-dev_0.0+git20160702.2610e25-7_armhf.deb 3657cb95290e379ea179a909034301075e009390 396140 libsmithwaterman0-dbgsym_0.0+git20160702.2610e25-7_armhf.deb 3beda12c7cbbafdc6d9e50cd7736e6259e1f8e05 31416 libsmithwaterman0_0.0+git20160702.2610e25-7_armhf.deb 5800edb303e0f64df6cbe2d4c41e26634e4cc048 6280 libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo 392e2ff13d1b2ce8dc848fed7fd8a3624e168a29 68784 smithwaterman-dbgsym_0.0+git20160702.2610e25-7_armhf.deb a77cf24ac6b32ca80fddfa6d800e965ff4b9748d 8980 smithwaterman_0.0+git20160702.2610e25-7_armhf.deb Checksums-Sha256: 078a03f2858c2d0fd31c32e18972fbb04e6535f0d97e8b0ab9b8e48a6e925951 36088 libsmithwaterman-dev_0.0+git20160702.2610e25-7_armhf.deb f08465919f153920843c37002faf4e4ae7293818b7a608cba67cd45e55d79c7f 396140 libsmithwaterman0-dbgsym_0.0+git20160702.2610e25-7_armhf.deb 174f319b6e52d9cf1f1b8c6c1f71027ff44844fe71e616c066765e5f22d6e7a6 31416 libsmithwaterman0_0.0+git20160702.2610e25-7_armhf.deb ab6f34786e2595c6724e33498efe32440bb35391f1b0881704512a4873671c34 6280 libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo 2fcdbd04f73a2d4b1abb9fc3a8e50d2c3f3c0f73b73393733e963bf8e871ca87 68784 smithwaterman-dbgsym_0.0+git20160702.2610e25-7_armhf.deb a7b18dc315d2d5deb3c1f306aa02777dbccc2e2fe0f05e8704b110b080ba2256 8980 smithwaterman_0.0+git20160702.2610e25-7_armhf.deb Files: c075803fc1cc8b1ab0d5ee1986db92a9 36088 libdevel optional libsmithwaterman-dev_0.0+git20160702.2610e25-7_armhf.deb a8ef318818ccc7126619733faf956137 396140 debug optional libsmithwaterman0-dbgsym_0.0+git20160702.2610e25-7_armhf.deb 0d8c48391936f4e348b6d20197551afa 31416 libs optional libsmithwaterman0_0.0+git20160702.2610e25-7_armhf.deb bf77a861c17700908864b93c3755cf96 6280 science optional libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo 1b9b48eef64104493ab19973229a569d 68784 debug optional smithwaterman-dbgsym_0.0+git20160702.2610e25-7_armhf.deb 7338c03087b1283691e90db953a04ade 8980 science optional smithwaterman_0.0+git20160702.2610e25-7_armhf.deb Thu Oct 8 03:05:05 UTC 2020 I: diffoscope 160 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/libsmithwaterman_0.0+git20160702.2610e25-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/libsmithwaterman_0.0+git20160702.2610e25-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/libsmithwaterman_0.0+git20160702.2610e25-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/b1/libsmithwaterman_0.0+git20160702.2610e25-7_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.yUgYwbppuB/b2/libsmithwaterman_0.0+git20160702.2610e25-7_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: 0.201s) 0.201s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.029s) 0.029s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Oct 8 03:05:07 UTC 2020 I: diffoscope 160 found no differences in the changes files, and a .buildinfo file also exists. Thu Oct 8 03:05:07 UTC 2020 I: libsmithwaterman from buster built successfully and reproducibly on armhf. Thu Oct 8 03:05:08 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Oct 8 03:05:08 UTC 2020 I: Submitting 8.0K b1/libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo.asc Thu Oct 8 03:05:10 UTC 2020 I: Submitting 8.0K b2/libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo.asc Thu Oct 8 03:05:10 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Oct 8 03:05:10 UTC 2020 I: Done submitting .buildinfo files. Thu Oct 8 03:05:10 UTC 2020 I: Removing signed libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo.asc files: removed './b1/libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo.asc' removed './b2/libsmithwaterman_0.0+git20160702.2610e25-7_armhf.buildinfo.asc'