Sun Aug 16 02:55:21 UTC 2020 I: starting to build tophat/buster/arm64 on jenkins on '2020-08-16 02:55' Sun Aug 16 02:55:21 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/908/console.log Sun Aug 16 02:55:21 UTC 2020 I: Downloading source for buster/tophat=2.1.1+dfsg1-2 --2020-08-16 02:55:21-- http://deb.debian.org/debian/pool/main/t/tophat/tophat_2.1.1+dfsg1-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) Saving to: ‘tophat_2.1.1+dfsg1-2.dsc’ 0K .. 100% 259M=0s 2020-08-16 02:55:21 (259 MB/s) - ‘tophat_2.1.1+dfsg1-2.dsc’ saved [2184/2184] Sun Aug 16 02:55:21 UTC 2020 I: tophat_2.1.1+dfsg1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tophat Binary: tophat Architecture: any Version: 2.1.1+dfsg1-2 Maintainer: Debian Med Packaging Team Uploaders: Carlos Borroto , Alexandre Mestiashvili , Andreas Tille Homepage: http://ccb.jhu.edu/software/tophat Standards-Version: 4.2.0 Vcs-Browser: https://salsa.debian.org/med-team/tophat Vcs-Git: https://salsa.debian.org/med-team/tophat.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie Package-List: tophat deb science optional arch=any Checksums-Sha1: 3069f6eb5159064a49d0a1f41b570e7ff56be9bd 349996 tophat_2.1.1+dfsg1.orig.tar.xz 26f4696a5f2c785711e2b61ec51e9dfc04c183b5 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz Checksums-Sha256: 16c1b414e8dcb6bb241cc7560d1e7495f00b39fd0ef5b2c3d09e19c1685219c3 349996 tophat_2.1.1+dfsg1.orig.tar.xz 34b340161a2340e6acb44968bf4adaaf43b02e74412441b11f0dc20dde2283ce 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz Files: 9e350c80adba6b6fdc8045ef4e085800 349996 tophat_2.1.1+dfsg1.orig.tar.xz 5072d66e095477f87ce398ccfd02098f 18636 tophat_2.1.1+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlt3y6wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHrYw//bxAuZXH2PYThUeeT9evLGxgJtc+GfxoJ da6D3XLsyhyF2O3BwaN9FJfvo3hakzaQRYf4DDXzLsfYKFnmQvrpgpZ09NTLCN5x yhwds1ZprEfSFm9xqH9XGC5Zrhv9/Yv1q8EtiGuEUr6CQvh9UKcmZA/Q3edlumDb oE3LhzMG/iWiUXZwRn0YS0qj85yTQKB9K+be9Z7vjqVqU3kEwqDvBs3GSBWfd03W +/+4OQC6toZ37AgocFzJtWAfVQl6pfWTLfHtX7W2aeWJEHj7AzVbemYndzStAklg +erwoEBgMBfN/JMxGvSn9g+FhJTfFXKcMtNcH4mt4g+6zv90ovde3BxGDCLEh1HK IFjIx9jqEgdS6CoJZANkC5wdbdTD2oCALT3Qcu2QdsDKL1x4icrDyqoUN5OQKrEo myvH4TGknLWFtfMKUEekNvvVTdAGrocFmSPXhaviFQ+zF7BntJOKBcI7Yq+z4Xlm aIfd1yC6pNJ7RNkrE2xQ1CcrzrZzkwoCrIr03k7y4CcuURMC56Rk0qxNQDB6dMX6 1eLxoBhRYrOxTqZrpf4+Ule3A52V61ZSwDSvSvWJRnFAZrh8RIehukJi3lGT3ip2 4NPp04aAznjvwk/e2LYnjPrXK91mn+srmCG3rfwHkCxVJoP4A4QLAwQq7FXlTRq3 8twRndXKRyU= =6hDw -----END PGP SIGNATURE----- Sun Aug 16 02:55:21 UTC 2020 I: Checking whether the package is not for us Sun Aug 16 02:55:21 UTC 2020 I: Starting 1st build on remote node codethink-sled11-arm64.debian.net. Sun Aug 16 02:55:21 UTC 2020 I: Preparing to do remote build '1' on codethink-sled11-arm64.debian.net. Sun Aug 16 03:03:03 UTC 2020 I: Deleting $TMPDIR on codethink-sled11-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 17 21:18:29 -12 2021 I: pbuilder-time-stamp: 1631956709 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 [tophat_2.1.1+dfsg1-2.dsc] I: copying [./tophat_2.1.1+dfsg1.orig.tar.xz] I: copying [./tophat_2.1.1+dfsg1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Aug 17 19:33:00 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tophat_2.1.1+dfsg1-2.dsc dpkg-source: info: extracting tophat in tophat-2.1.1+dfsg1 dpkg-source: info: unpacking tophat_2.1.1+dfsg1.orig.tar.xz dpkg-source: info: unpacking tophat_2.1.1+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_3rd_party_code.patch dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying fix-gcc6.patch dpkg-source: info: applying remove-convenience-copy-of-samtools.patch dpkg-source: info: applying fix-compatibility-with-recent-samtools.patch dpkg-source: info: applying fix_makefile.am.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31306/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 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='31306' 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.dQYbFMkLtJ/pbuilderrc_4XhW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/b1 --logfile b1/build.log tophat_2.1.1+dfsg1-2.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 codethink-sled11-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 17 02:49 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 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/31306/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 (>= 11~), libbam-dev, zlib1g-dev, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man, bowtie dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on seqan-dev (>= 1.4); however: Package seqan-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on bowtie; however: Package bowtie 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} bowtie{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtbb2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} seqan-dev{a} zlib1g-dev{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, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 38.6 MB of archives. After unpacking 266 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libtbb2 arm64 2018~U6-4 [122 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 bowtie arm64 1.2.2+dfsg-4 [1275 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libbam-dev arm64 0.1.19-4 [119 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libboost-atomic1.67.0 arm64 1.67.0-13+deb10u1 [226 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libboost-atomic1.67-dev arm64 1.67.0-13+deb10u1 [225 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libboost-chrono1.67.0 arm64 1.67.0-13+deb10u1 [233 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libboost-chrono1.67-dev arm64 1.67.0-13+deb10u1 [235 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libboost-date-time1.67.0 arm64 1.67.0-13+deb10u1 [238 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67.0 arm64 1.67.0-13+deb10u1 [311 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67-dev arm64 1.67.0-13+deb10u1 [358 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libboost-date-time1.67-dev arm64 1.67.0-13+deb10u1 [248 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libboost-system1.67-dev arm64 1.67.0-13+deb10u1 [231 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libboost-system-dev arm64 1.67.0.1 [3788 B] Get: 65 http://deb.debian.org/debian buster/main arm64 libboost-thread1.67.0 arm64 1.67.0-13+deb10u1 [264 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libboost-thread1.67-dev arm64 1.67.0-13+deb10u1 [270 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libboost-thread-dev arm64 1.67.0.1 [3672 B] Get: 68 http://deb.debian.org/debian buster/main arm64 seqan-dev all 1.4.2+dfsg-3 [1096 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 38.6 MB in 3s (11.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. 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Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20664 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_arm64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../04-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../07-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... 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Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-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 .../18-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 .../19-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../20-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../21-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../22-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../23-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../25-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../26-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.47.8_arm64.deb ... Unpacking help2man (1.47.8) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../32-libbam-dev_0.1.19-4_arm64.deb ... Unpacking libbam-dev (0.1.19-4) ... Selecting previously unselected package libboost1.67-dev:arm64. Preparing to unpack .../33-libboost1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-atomic1.67.0:arm64. Preparing to unpack .../34-libboost-atomic1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-atomic1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-atomic1.67-dev:arm64. Preparing to unpack .../35-libboost-atomic1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-atomic1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-chrono1.67.0:arm64. Preparing to unpack .../36-libboost-chrono1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-chrono1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-chrono1.67-dev:arm64. Preparing to unpack .../37-libboost-chrono1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-chrono1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-date-time1.67.0:arm64. Preparing to unpack .../38-libboost-date-time1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-date-time1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-serialization1.67.0:arm64. Preparing to unpack .../39-libboost-serialization1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-serialization1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-serialization1.67-dev:arm64. Preparing to unpack .../40-libboost-serialization1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-serialization1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-date-time1.67-dev:arm64. Preparing to unpack .../41-libboost-date-time1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-date-time1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system1.67-dev:arm64. Preparing to unpack .../42-libboost-system1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-system1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system-dev:arm64. Preparing to unpack .../43-libboost-system-dev_1.67.0.1_arm64.deb ... Unpacking libboost-system-dev:arm64 (1.67.0.1) ... Selecting previously unselected package libboost-thread1.67.0:arm64. Preparing to unpack .../44-libboost-thread1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-thread1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-thread1.67-dev:arm64. Preparing to unpack .../45-libboost-thread1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-thread1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-thread-dev:arm64. Preparing to unpack .../46-libboost-thread-dev_1.67.0.1_arm64.deb ... Unpacking libboost-thread-dev:arm64 (1.67.0.1) ... Selecting previously unselected package seqan-dev. Preparing to unpack .../47-seqan-dev_1.4.2+dfsg-3_all.deb ... Unpacking seqan-dev (1.4.2+dfsg-3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../48-zlib1g-dev_1%3a1.2.11.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up libboost1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libexpat1:arm64 (2.2.6-2+deb10u1) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libboost-chrono1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libtbb2:arm64 (2018~U6-4) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libboost-date-time1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libboost-chrono1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libbam-dev (0.1.19-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libboost-atomic1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libboost-system1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libboost-serialization1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up seqan-dev (1.4.2+dfsg-3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libboost-atomic1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libboost-serialization1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libboost-thread1.67.0:arm64 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-system-dev:arm64 (1.67.0.1) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up help2man (1.47.8) ... Setting up libboost-date-time1.67-dev:arm64 (1.67.0-13+deb10u1) ... 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:arm64 (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 python2.7 (2.7.16-2+deb10u1) ... Setting up libboost-thread1.67-dev:arm64 (1.67.0-13+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libboost-thread-dev:arm64 (1.67.0.1) ... Setting up bowtie (1.2.2+dfsg-4) ... 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/tophat-2.1.1+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package tophat dpkg-buildpackage: info: source version 2.1.1+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found configure.ac:20: installing './compile' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/tophat-2.1.1+dfsg1' dh_auto_configure -- --with-boost-libdir=/usr/lib/aarch64-linux-gnu ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/aarch64-linux-gnu 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 for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc 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 ar... ar checking the archiver (ar) interface... ar checking for gawk... (cached) mawk checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... yes checking how to run the C++ preprocessor... g++ -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 for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode -- tophat 2.1.1 Configuration Results -- C++ compiler: g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include Linker flags: -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now BOOST libraries: -lboost_thread -lboost_system GCC version: gcc (Debian 8.3.0-6) 8.3.0 Host System type: aarch64-unknown-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . make[1]: Leaving directory '/build/tophat-2.1.1+dfsg1' dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/tophat-2.1.1+dfsg1' make all-recursive make[2]: Entering directory '/build/tophat-2.1.1+dfsg1' Making all in src make[3]: Entering directory '/build/tophat-2.1.1+dfsg1/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o prep_reads.o prep_reads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o reads.o reads.cpp gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bwt_map.o bwt_map.cpp bwt_map.cpp: In function 'bool spliceCigar(std::vector&, const std::vector&, std::vector, int&, int, int, CigarOpCode, int&)': bwt_map.cpp:705:9: warning: variable 'prev_opcode' set but not used [-Wunused-but-set-variable] int prev_opcode=0; ^~~~~~~~~~~ bwt_map.cpp:706:9: warning: variable 'prev_oplen' set but not used [-Wunused-but-set-variable] int prev_oplen=0; ^~~~~~~~~~ bwt_map.cpp: In member function 'virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)': bwt_map.cpp:1112:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable] int text_mate_pos = hit_buf->core.mpos; ^~~~~~~~~~~~~ bwt_map.cpp:1118:7: warning: variable 'num_hits' set but not used [-Wunused-but-set-variable] int num_hits = 1; ^~~~~~~~ bwt_map.cpp: In member function 'virtual bool SplicedBAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)': bwt_map.cpp:1481:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable] int text_mate_pos = hit_buf->core.mpos; ^~~~~~~~~~~~~ bwt_map.cpp:1486:8: warning: variable 'spliced_alignment' set but not used [-Wunused-but-set-variable] bool spliced_alignment = false; ^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp common.cpp: In member function 'std::__cxx11::string GBamRecord::seqData(std::__cxx11::string*)': common.cpp:1259:8: warning: variable 'mate_num' set but not used [-Wunused-but-set-variable] int mate_num=0; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o junctions.o junctions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o insertions.o insertions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o deletions.o deletions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fusions.o fusions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o align_status.o align_status.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fragments.o fragments.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o inserts.o inserts.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o qual.o qual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam_merge_impl.o bam_merge_impl.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o coverage.o coverage.cpp rm -f libtophat.a ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libtophat.a g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o prep_reads prep_reads.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GTFToFasta.o GTFToFasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o FastaTools.o FastaTools.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GBase.o GBase.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GStr.o GStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gff.o gff.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gff.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GffCDSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GffCDSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GffCDSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GffCDSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GffCDSeg]' gff.cpp:2117:22: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffCDSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.cpp:1: gff.h:427:7: note: 'class GffCDSeg' declared here class GffCDSeg:public GSeg { ^~~~~~~~ rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgc.a g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o gtf_to_fasta GTFToFasta.o FastaTools.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o fix_map_ordering.o fix_map_ordering.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o fix_map_ordering fix_map_ordering.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam2fastx.o bam2fastx.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o segment_juncs.o segment_juncs.cpp segment_juncs.cpp: In member function 'void SegmentSearchWorker::operator()()': segment_juncs.cpp:4625:27: warning: variable 'last_read_id' set but not used [-Wunused-but-set-variable] uint64_t read_id = 0, last_read_id = 0; ^~~~~~~~~~~~ g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o segment_juncs segment_juncs.o libtophat.a -lboost_thread -lboost_system -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gtf_juncs.o gtf_juncs.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o gtf_juncs gtf_juncs.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o juncs_db.o juncs_db.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o juncs_db juncs_db.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o long_spanning_reads.o long_spanning_reads.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o long_spanning_reads long_spanning_reads.o libtophat.a -lboost_thread -lboost_system -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bam_merge.o bam_merge.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o bam_merge bam_merge.o libtophat.a ../src/libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o map2gtf.o map2gtf.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o map2gtf map2gtf.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o tophat_reports tophat_reports.o libtophat.a -lboost_thread -lboost_system -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o sam_juncs.o sam_juncs.cpp g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -ffile-prefix-map=/build/tophat-2.1.1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -o sam_juncs sam_juncs.o libtophat.a -lbam -lz cp tophat2.sh tophat2 && chmod 755 tophat2 sed -e 's|__VERSION__|2.1.1|' tophat.py > tophat && chmod 755 tophat make[3]: Leaving directory '/build/tophat-2.1.1+dfsg1/src' make[3]: Entering directory '/build/tophat-2.1.1+dfsg1' make[3]: Leaving directory '/build/tophat-2.1.1+dfsg1' make[2]: Leaving directory '/build/tophat-2.1.1+dfsg1' make[1]: Leaving directory '/build/tophat-2.1.1+dfsg1' dh_auto_test -O--no-parallel make -j1 check VERBOSE=1 make[1]: Entering directory '/build/tophat-2.1.1+dfsg1' Making check in src make[2]: Entering directory '/build/tophat-2.1.1+dfsg1/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/tophat-2.1.1+dfsg1/src' make[2]: Entering directory '/build/tophat-2.1.1+dfsg1' make[2]: Leaving directory '/build/tophat-2.1.1+dfsg1' make[1]: Leaving directory '/build/tophat-2.1.1+dfsg1' 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/tophat-2.1.1\+dfsg1/debian/tophat AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/tophat-2.1.1+dfsg1' Making install in src make[2]: Entering directory '/build/tophat-2.1.1+dfsg1/src' make[3]: Entering directory '/build/tophat-2.1.1+dfsg1/src' /bin/mkdir -p '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' /usr/bin/install -c prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' /bin/mkdir -p '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' /usr/bin/install -c tophat2 tophat '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' /bin/mkdir -p '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' /usr/bin/install -c contig_to_chr_coords bed_to_juncs sra_to_solid tophat-fusion-post '/build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/tophat-2.1.1+dfsg1/src' make[2]: Leaving directory '/build/tophat-2.1.1+dfsg1/src' make[2]: Entering directory '/build/tophat-2.1.1+dfsg1' make[3]: Entering directory '/build/tophat-2.1.1+dfsg1' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/tophat-2.1.1+dfsg1' make[2]: Leaving directory '/build/tophat-2.1.1+dfsg1' make[1]: Leaving directory '/build/tophat-2.1.1+dfsg1' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel debian/rules override_dh_installman make[1]: Entering directory '/build/tophat-2.1.1+dfsg1' dh_installman # try to create man pages whereever possible mkdir -p /build/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1 help2man --no-info --no-discard-stderr -h "" \ --name='tophat component converting bam directly into fastx' \ --version-string="2.1.1+dfsg1-2" \ /build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/bam2fastx > /build/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/bam2fastx.1 help2man --no-info --no-discard-stderr -h "-h" \ --name='tophat component to convert junctions in BED format' \ --version-string="2.1.1+dfsg1-2" \ /build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/bed_to_juncs > /build/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/bed_to_juncs.1 help2man --no-info --no-discard-stderr -h "-h" \ --name='tophat component taking NCBI seq_contig file and maps contig coords' \ --version-string="2.1.1+dfsg1-2" \ /build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/contig_to_chr_coords > /build/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/contig_to_chr_coords.1 help2man --no-info --no-discard-stderr \ --name='TopHat maps short sequences from spliced transcripts to whole genomes' \ --version-string="2.1.1+dfsg1-2" \ /build/tophat-2.1.1+dfsg1/debian/tophat/usr/bin/tophat > /build/tophat-2.1.1+dfsg1/debian/tophat/usr/share/man/man1/tophat.1 make[1]: Leaving directory '/build/tophat-2.1.1+dfsg1' 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 dh_shlibdeps -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'tophat' in '../tophat_2.1.1+dfsg1-2_arm64.deb'. dpkg-deb: building package 'tophat-dbgsym' in '../tophat-dbgsym_2.1.1+dfsg1-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tophat_2.1.1+dfsg1-2_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) 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/31306 and its subdirectories I: Current time: Fri Sep 17 21:25:55 -12 2021 I: pbuilder-time-stamp: 1631957155 Sun Aug 16 03:03:04 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled10-arm64.debian.net. Sun Aug 16 03:03:04 UTC 2020 I: Preparing to do remote build '2' on codethink-sled10-arm64.debian.net. Sun Aug 16 03:09:13 UTC 2020 I: Deleting $TMPDIR on codethink-sled10-arm64.debian.net. Sun Aug 16 03:09:14 UTC 2020 I: tophat_2.1.1+dfsg1-2_arm64.changes: Format: 1.8 Date: Sat, 18 Aug 2018 09:28:30 +0200 Source: tophat Binary: tophat tophat-dbgsym Architecture: arm64 Version: 2.1.1+dfsg1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tophat - fast splice junction mapper for RNA-Seq reads Closes: 906510 Changes: tophat (2.1.1+dfsg1-2) unstable; urgency=medium . * Fix Makefile.am Closes: #906510 * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.0 * Remove unneeded get-orig-source target Checksums-Sha1: 34e3d11bd546abc0b834a1d7fe08698d80d96c3a 10395616 tophat-dbgsym_2.1.1+dfsg1-2_arm64.deb 250002e7be610c3eaf0eac21791b4ddde993a540 6017 tophat_2.1.1+dfsg1-2_arm64.buildinfo fa2dd7fad71ee788e6693d8f961b1650c9b7588b 609636 tophat_2.1.1+dfsg1-2_arm64.deb Checksums-Sha256: 3d3da3cd9777fd7d03210eb4362c32c9c3790c42ff0b5f24236f0d1917f0a92a 10395616 tophat-dbgsym_2.1.1+dfsg1-2_arm64.deb 6501b1a9634ae7e3472c2aff01b453449e09c94f1303908ef46cfb69486c7a3f 6017 tophat_2.1.1+dfsg1-2_arm64.buildinfo 51f3628e150039271657ad140f9ed91780e7fe335fcead7c5a929ef3c6b1abf3 609636 tophat_2.1.1+dfsg1-2_arm64.deb Files: 2cba8489bdf099e6cbf1f89493d7eb86 10395616 debug optional tophat-dbgsym_2.1.1+dfsg1-2_arm64.deb 999bea8318448f2c4f882577e11d58c2 6017 science optional tophat_2.1.1+dfsg1-2_arm64.buildinfo 96fb724b72d9da1f0c8c5b5a1c649bdb 609636 science optional tophat_2.1.1+dfsg1-2_arm64.deb Sun Aug 16 03:09:15 UTC 2020 I: diffoscope 156 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/tophat_2.1.1+dfsg1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/tophat_2.1.1+dfsg1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/tophat_2.1.1+dfsg1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/b1/tophat_2.1.1+dfsg1-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.dQYbFMkLtJ/b2/tophat_2.1.1+dfsg1-2_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: 0.339s) 0.339s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.121s) 0.121s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Aug 16 03:09:16 UTC 2020 I: diffoscope 156 found no differences in the changes files, and a .buildinfo file also exists. Sun Aug 16 03:09:16 UTC 2020 I: tophat from buster built successfully and reproducibly on arm64. Sun Aug 16 03:09:18 UTC 2020 I: Submitting .buildinfo files to external archives: Sun Aug 16 03:09:18 UTC 2020 I: Submitting 8.0K b1/tophat_2.1.1+dfsg1-2_arm64.buildinfo.asc Sun Aug 16 03:09:19 UTC 2020 I: Submitting 8.0K b2/tophat_2.1.1+dfsg1-2_arm64.buildinfo.asc Sun Aug 16 03:09:20 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Aug 16 03:09:20 UTC 2020 I: Done submitting .buildinfo files. Sun Aug 16 03:09:20 UTC 2020 I: Removing signed tophat_2.1.1+dfsg1-2_arm64.buildinfo.asc files: removed './b1/tophat_2.1.1+dfsg1-2_arm64.buildinfo.asc' removed './b2/tophat_2.1.1+dfsg1-2_arm64.buildinfo.asc'