Wed Aug 26 20:11:39 UTC 2020 I: starting to build cd-hit/buster/arm64 on jenkins on '2020-08-26 20:11' Wed Aug 26 20:11:39 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/3550/console.log Wed Aug 26 20:11:40 UTC 2020 I: Downloading source for buster/cd-hit=4.6.8-2 --2020-08-26 20:11:41-- http://deb.debian.org/debian/pool/main/c/cd-hit/cd-hit_4.6.8-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1974 (1.9K) Saving to: ‘cd-hit_4.6.8-2.dsc’ 0K . 100% 105M=0s 2020-08-26 20:11:41 (105 MB/s) - ‘cd-hit_4.6.8-2.dsc’ saved [1974/1974] Wed Aug 26 20:11:42 UTC 2020 I: cd-hit_4.6.8-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: cd-hit Binary: cd-hit Architecture: any Version: 4.6.8-2 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/cd-hit Vcs-Git: https://salsa.debian.org/med-team/cd-hit.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), help2man Package-List: cd-hit deb science optional arch=any Checksums-Sha1: 2461b9e00069e2317394c7eae32ac5523777d975 932535 cd-hit_4.6.8.orig.tar.gz 648f55df138b889526813a9ec36717b1589e11ca 7528 cd-hit_4.6.8-2.debian.tar.xz Checksums-Sha256: 37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949 932535 cd-hit_4.6.8.orig.tar.gz af54566928dd3b94cbfea4e927207476bcf1922a68a54a8c3c79c45c6b2520e1 7528 cd-hit_4.6.8-2.debian.tar.xz Files: bdd73ec0cceab6653aab7b31b57c5a8b 932535 cd-hit_4.6.8.orig.tar.gz 608b59c68452fdc1b59a4575ec8c5a4d 7528 cd-hit_4.6.8-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlurIEgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGzsQ/+JT0hi0uJDpqX9swCbI51BQrJKpmrnkAj rYRMc0YpmXkSGXkJ3Pig0sHnSdxKZvpcz7D7GnoGTkLHmYz1ruA7VANFJ342s1Y+ HHkh9NT7pLPjDP2tFXX+cWpqOqpfc+8tQEX476nYe7encxk0eEwpb5D/+fn8OX5e rz/jzIEHX3QNSn8zykWRKuI+vbDEtirI7U3xelEkLoWy/yu46TQn8H3Cj+mJJWwd prS48W/aL/i3RkL6Qqme78eYcVaqXSsFmC7sVFkzzELVejJHRnbL7RRCIJJyFA4i Dsyb0iv+8vUxZ39hy5Ew6UMVaQMmrMRKuC+G8bP46pQlcvMqJqsNJMWK//XsA5Jv 6oi3aItmuUbKAgz7lIc8HKGVUbTz+fKZSWRS8V5o4hgajlzzmkKRe3OYV++ehgoP 8H1keFzcrjAGGhuEdMqx45WzrsP51BXb2nqy4eiboSPbiMte69YcsA3bj2FKFNUd IPmLlQ+2bvifZNMvePP/qftPq+BLWknc11msroVutJVhTrptUwpmOUU5nRo2PAfD eIrSoU9rWgukDD0e+id0Yb7I1rP+7rc25yOHnT3CBqv2K+TFOcg4HtU16dy0H1g+ qzNURe65RPLZWIE+DEWfyA7HpLFUDGG7ScqUpBt6xgHFQe1DrmGQNTY8JjNmpTqI zO5dADZ8cAM= =lAog -----END PGP SIGNATURE----- Wed Aug 26 20:11:42 UTC 2020 I: Checking whether the package is not for us Wed Aug 26 20:11:42 UTC 2020 I: Starting 1st build on remote node codethink-sled10-arm64.debian.net. Wed Aug 26 20:11:42 UTC 2020 I: Preparing to do remote build '1' on codethink-sled10-arm64.debian.net. Wed Aug 26 20:14:22 UTC 2020 I: Deleting $TMPDIR on codethink-sled10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 26 08:11:53 -12 2020 I: pbuilder-time-stamp: 1598472713 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 [cd-hit_4.6.8-2.dsc] I: copying [./cd-hit_4.6.8.orig.tar.gz] I: copying [./cd-hit_4.6.8-2.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 Tue Sep 25 17:59:36 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 ./cd-hit_4.6.8-2.dsc dpkg-source: info: extracting cd-hit in cd-hit-4.6.8 dpkg-source: info: unpacking cd-hit_4.6.8.orig.tar.gz dpkg-source: info: unpacking cd-hit_4.6.8-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying enable_help2man.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26946/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='26946' 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.3a3yShmWeB/pbuilderrc_u7TW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/b1 --logfile b1/build.log cd-hit_4.6.8-2.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-sled10-arm64 4.4.0-187-generic #217-Ubuntu SMP Tue Jul 21 04:16:35 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 07:38 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 Aug 23 20:27 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 07:38 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/26946/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~), help2man 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 help2man; however: Package help2man 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} 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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{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, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After unpacking 69.7 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 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Fetched 18.8 MB in 1s (13.9 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 liblocale-gettext-perl. Preparing to unpack .../06-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 .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-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 .../09-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-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 .../12-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... 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:arm64. Preparing to unpack .../23-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../25-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 .../26-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... 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Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... 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 help2man (1.47.8) ... 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 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/cd-hit-4.6.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package cd-hit dpkg-buildpackage: info: source version 4.6.8-2 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 dh_auto_clean make -j8 clean make[1]: Entering directory '/build/cd-hit-4.6.8' rm -f *.o cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 make[1]: Leaving directory '/build/cd-hit-4.6.8' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/cd-hit-4.6.8' dh_auto_build -- openmp=yes make -j8 "INSTALL=install --strip-program=true" openmp=yes make[2]: Entering directory '/build/cd-hit-4.6.8' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-common.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-utility.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.c++ -c cdhit-common.c++:322:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] strcpy( date, __DATE__ ); ^~~~~~~~ cdhit-utility.c++:9:79: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] char cd_hit_ver[] = "\t\t====== CD-HIT version " CDHIT_VERSION " (built on " __DATE__ ") ======"; ^~~~~~~~ cdhit-common.c++:326:66: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] printf( "Program: CD-HIT, V" CDHIT_VERSION WITH_OPENMP ", %s, " __TIME__ "\n", date ); ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-est g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-2d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-est-2d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-div g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.6.8=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-454 make[2]: Leaving directory '/build/cd-hit-4.6.8' make[1]: Leaving directory '/build/cd-hit-4.6.8' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/cd-hit-4.6.8' dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit make -j8 install DESTDIR=/build/cd-hit-4.6.8/debian/cd-hit AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/cd-hit/usr/lib/cd-hit make[2]: Entering directory '/build/cd-hit-4.6.8' for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \ install -m 0755 $prog debian/cd-hit/usr/lib/cd-hit; \ done install -m 0755 *.pl debian/cd-hit/usr/lib/cd-hit; make[2]: Leaving directory '/build/cd-hit-4.6.8' make[1]: Leaving directory '/build/cd-hit-4.6.8' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/cd-hit-4.6.8' mkdir -p /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1/ help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='quickly group sequences' \ /build/cd-hit-4.6.8/cd-hit > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='quickly group sequences, optimised for 454 data' \ /build/cd-hit-4.6.8/cd-hit-454 > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-454.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='quickly group sequences in db1 or db2 format' \ /build/cd-hit-4.6.8/cd-hit-2d > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='run CD-HIT algorithm on RNA/DNA sequences' \ /build/cd-hit-4.6.8/cd-hit-est > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-est.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \ /build/cd-hit-4.6.8/cd-hit-est-2d > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-est-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \ /build/cd-hit-4.6.8/cd-hit-2d-para.pl > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \ /build/cd-hit-4.6.8/cd-hit-para.pl > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-para.1 help2man --no-info --no-discard-stderr --version-string='4.6.8' \ --name='divide a FASTA file into pieces' \ /build/cd-hit-4.6.8/cd-hit-div.pl > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//cd-hit-div.1 # psi-cd-hit.pl is throwing some errors which are fixed using sed # ... at least in versions <= 4.6.4 - now help2man does not work at all #help2man --no-info --no-discard-stderr --version-string='4.6.8' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \ # /build/cd-hit-4.6.8/psi-cd-hit.pl | \ # sed -e '/^Name "main::.*" used only once:/d' \ # > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//psi-cd-hit.1 # help2man does not work at all since version 4.6.4 #help2man --no-info --no-discard-stderr --version-string='4.6.8' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ # /build/cd-hit-4.6.8/psi-cd-hit-2d.pl > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d.1 # FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ? # help2man does not work at all since version 4.6.4 #help2man --no-info --no-discard-stderr --version-string='4.6.8' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ # /build/cd-hit-4.6.8/psi-cd-hit-2d-g1.pl > /build/cd-hit-4.6.8/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d-g1.1 # No help output from # clstr2tree.pl # clstr_merge.pl # clstr_merge_noorder.pl # clstr_reduce.pl # clstr_renumber.pl # clstr_rev.pl # clstr_sort_by.pl # clstr_sort_prot_by # make_multi_seq # psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors make[1]: Leaving directory '/build/cd-hit-4.6.8' dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/cd-hit-4.6.8' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/cd-hit-4.6.8' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/cd-hit/usr/lib/cd-hit/cd-hit-div debian/cd-hit/usr/lib/cd-hit/cd-hit-est debian/cd-hit/usr/lib/cd-hit/cd-hit-2d debian/cd-hit/usr/lib/cd-hit/cd-hit debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d debian/cd-hit/usr/lib/cd-hit/cd-hit-454 were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cd-hit-dbgsym' in '../cd-hit-dbgsym_4.6.8-2_arm64.deb'. dpkg-deb: building package 'cd-hit' in '../cd-hit_4.6.8-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cd-hit_4.6.8-2_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/26946 and its subdirectories I: Current time: Wed Aug 26 08:14:18 -12 2020 I: pbuilder-time-stamp: 1598472858 Wed Aug 26 20:14:23 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled11-arm64.debian.net. Wed Aug 26 20:14:23 UTC 2020 I: Preparing to do remote build '2' on codethink-sled11-arm64.debian.net. Wed Aug 26 20:15:23 UTC 2020 I: Deleting $TMPDIR on codethink-sled11-arm64.debian.net. Wed Aug 26 20:15:24 UTC 2020 I: cd-hit_4.6.8-2_arm64.changes: Format: 1.8 Date: Wed, 19 Sep 2018 14:47:50 +0200 Source: cd-hit Binary: cd-hit cd-hit-dbgsym Architecture: arm64 Version: 4.6.8-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: cd-hit - suite of programs designed to quickly group sequences Changes: cd-hit (4.6.8-2) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 70cd8c725f00c8460fd02d4c8c9940533886b75c 2562556 cd-hit-dbgsym_4.6.8-2_arm64.deb 7c9c88b03b08e8988f575d27b171a558dfbbb0f4 4632 cd-hit_4.6.8-2_arm64.buildinfo 2f13172d4df4626b4272152849137e10f3638440 503548 cd-hit_4.6.8-2_arm64.deb Checksums-Sha256: 0bcbebe12f9989bf54a3b44229c189be86a4488e4464c4a48d2fc802a6bbb310 2562556 cd-hit-dbgsym_4.6.8-2_arm64.deb 7f2b14aaa5de7aa0c789bdb16c7e16ca53d6684ec900ed1acddafbd065c7f6e8 4632 cd-hit_4.6.8-2_arm64.buildinfo 78b566ef44a017da2fa5d312d0f70b7a3a7594810cc906856618407537075da2 503548 cd-hit_4.6.8-2_arm64.deb Files: d2bdd20222b5c80221eb741083c5373f 2562556 debug optional cd-hit-dbgsym_4.6.8-2_arm64.deb 5f9b3757359efba3f7e0425ef7f3feb9 4632 science optional cd-hit_4.6.8-2_arm64.buildinfo c7d65f004b35c80fd90e5aa26e75a53d 503548 science optional cd-hit_4.6.8-2_arm64.deb Wed Aug 26 20:15:25 UTC 2020 I: diffoscope 157 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/cd-hit_4.6.8-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/cd-hit_4.6.8-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/cd-hit_4.6.8-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/b1/cd-hit_4.6.8-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.3a3yShmWeB/b2/cd-hit_4.6.8-2_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: 0.260s) 0.260s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.056s) 0.056s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Aug 26 20:15:27 UTC 2020 I: diffoscope 157 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 26 20:15:27 UTC 2020 I: cd-hit from buster built successfully and reproducibly on arm64. Wed Aug 26 20:15:29 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Aug 26 20:15:29 UTC 2020 I: Submitting 8.0K b1/cd-hit_4.6.8-2_arm64.buildinfo.asc Wed Aug 26 20:15:30 UTC 2020 I: Submitting 8.0K b2/cd-hit_4.6.8-2_arm64.buildinfo.asc Wed Aug 26 20:15:31 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Aug 26 20:15:31 UTC 2020 I: Done submitting .buildinfo files. Wed Aug 26 20:15:31 UTC 2020 I: Removing signed cd-hit_4.6.8-2_arm64.buildinfo.asc files: removed './b1/cd-hit_4.6.8-2_arm64.buildinfo.asc' removed './b2/cd-hit_4.6.8-2_arm64.buildinfo.asc'