Wed May 3 13:13:48 UTC 2023 I: starting to build cd-hit/bookworm/amd64 on jenkins on '2023-05-03 13:13' Wed May 3 13:13:48 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/9237/console.log Wed May 3 13:13:48 UTC 2023 I: Downloading source for bookworm/cd-hit=4.8.1-4 --2023-05-03 13:13:49-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/cd-hit/cd-hit_4.8.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2032 (2.0K) [text/prs.lines.tag] Saving to: ‘cd-hit_4.8.1-4.dsc’ 0K . 100% 191M=0s 2023-05-03 13:13:49 (191 MB/s) - ‘cd-hit_4.8.1-4.dsc’ saved [2032/2032] Wed May 3 13:13:49 UTC 2023 I: cd-hit_4.8.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cd-hit Binary: cd-hit Architecture: any Version: 4.8.1-4 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille , Étienne Mollier Homepage: http://weizhongli-lab.org/cd-hit/ Standards-Version: 4.6.0 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-compat (= 13), help2man, zlib1g-dev Package-List: cd-hit deb science optional arch=any Checksums-Sha1: 12c401562cd506296ccafa301e1fd8a29b210470 945639 cd-hit_4.8.1.orig.tar.gz 0c7096447908bdbb0cb5795b02171c585d3618f0 8128 cd-hit_4.8.1-4.debian.tar.xz Checksums-Sha256: f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70 945639 cd-hit_4.8.1.orig.tar.gz 827e471b3724e5680aebf69c155d825aa812be549bf0536defc29668f3abbbe1 8128 cd-hit_4.8.1-4.debian.tar.xz Files: b997bcc5a07703ca9bd3f84818114c37 945639 cd-hit_4.8.1.orig.tar.gz 40beb397b78cc269ea9dc48f9fa22c88 8128 cd-hit_4.8.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmEfbYsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqkXBAAwMJobCyKBNsZS2dmYUeOST550IJT CeDXSEggmWF9Mw5Rkmazj7TWBRkk0YlhVPhCcJqHiVOnF2ZqP/39oRq7Gr9ZxRvd WkXWxTtJUhJ76sMedjgLxSN+5ymYWc5eTVeTaJnW3rhXRWKp4TSZ137LbRUwSwue SA2acrDl61yZYLP2NunGob882kAdDbWyiYLElvr8dZClEaOfMyCcla3sAwzxVSYW U5xbyTLuOOFI2PZoXcspmJhU/aKo6YtEYEQJKUckD3+RziXLNtbOIe7cvq4STRp7 N03vUNU81KDxjmkoQXMJLHDbyQjh61w6KkdTGCICuWGa9Ihxk3dKLCs4/B4h+yKo 2sSELDU9KDATXVtDS4ZdoFTPxaYgVahmaDQJwSOD958iq2QJoyhWyg+HAz55raPJ hBOu+kAIym6lGbmRsTRVkblFX0KgDZa19jzu+sfR7W3HBFNeWDPZMI65fykUU8HQ Kovkw+grEPeLiZiejk0tsV2x9VyCRsjRiBMwk/19QKvSbf34hgx6unRsiMHwwMSM SXOOqIQAz8PUWAAF2NXe3lSdaX69XFyB6W+unGrKnTAx6Uf8zNqzqGTYn6DG4tls YeGY/8TqU3JMWCUT7zNXAljxfYviGtg0Lme1WH3eFb2T/xKxUOLOGSitBQHD2YER XB4SNWSZft9uOFE= =0WHq -----END PGP SIGNATURE----- Wed May 3 13:13:49 UTC 2023 I: Checking whether the package is not for us Wed May 3 13:13:49 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed May 3 13:13:49 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed May 3 13:15:49 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 3 01:13:51 -12 2023 I: pbuilder-time-stamp: 1683119631 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_4.8.1-4.dsc] I: copying [./cd-hit_4.8.1.orig.tar.gz] I: copying [./cd-hit_4.8.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 19 20:53:31 2021 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cd-hit_4.8.1-4.dsc: no acceptable signature found dpkg-source: info: extracting cd-hit in cd-hit-4.8.1 dpkg-source: info: unpacking cd-hit_4.8.1.orig.tar.gz dpkg-source: info: unpacking cd-hit_4.8.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying enable_help2man.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2885057/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5837e0a6ca534a2fbc2bce798423075e' 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='2885057' 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/r-b-build.IhdQqEuf/pbuilderrc_r0I0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/b1 --logfile b1/build.log cd-hit_4.8.1-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2885057/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), help2man, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After unpacking 74.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 19.9 MB in 1s (22.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. 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Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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 I: Building the package I: Running cd /build/cd-hit-4.8.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cd-hit_4.8.1-4_source.changes dpkg-buildpackage: info: source package cd-hit dpkg-buildpackage: info: source version 4.8.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/cd-hit-4.8.1' 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-4.8.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/cd-hit-4.8.1' dh_auto_build -- openmp=yes CC='$(CXX)' make -j15 "INSTALL=install --strip-program=true" openmp=yes CC=\$\(CXX\) make[2]: Entering directory '/build/cd-hit-4.8.1' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-common.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-utility.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.c++ -c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.c++ -c cdhit-utility.c++:9:79: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 9 | char cd_hit_ver[] = "\t\t====== CD-HIT version " CDHIT_VERSION " (built on " __DATE__ ") ======"; | ^~~~~~~~ cdhit-common.c++:322:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 322 | strcpy( date, __DATE__ ); | ^~~~~~~~ cdhit-common.c++:326:73: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 326 | printf( "Program: CD-HIT, V" CDHIT_VERSION WITH_OPENMP ", %s, " __TIME__ "\n", date ); | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit-est g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit-2d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit-est-2d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit-div g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DWITH_ZLIB -O2 -g -O2 -ffile-prefix-map=/build/cd-hit-4.8.1=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -lz -o cd-hit-454 make[2]: Leaving directory '/build/cd-hit-4.8.1' make[1]: Leaving directory '/build/cd-hit-4.8.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/cd-hit-4.8.1' dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit make -j15 install DESTDIR=/build/cd-hit-4.8.1/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-4.8.1' 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-4.8.1' make[1]: Leaving directory '/build/cd-hit-4.8.1' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/cd-hit-4.8.1' mkdir -p /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1/ help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='quickly group sequences' \ /build/cd-hit-4.8.1/cd-hit > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='quickly group sequences, optimised for 454 data' \ /build/cd-hit-4.8.1/cd-hit-454 > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-454.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='quickly group sequences in db1 or db2 format' \ /build/cd-hit-4.8.1/cd-hit-2d > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-2d.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='run CD-HIT algorithm on RNA/DNA sequences' \ /build/cd-hit-4.8.1/cd-hit-est > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-est.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \ /build/cd-hit-4.8.1/cd-hit-est-2d > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-est-2d.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \ /build/cd-hit-4.8.1/cd-hit-2d-para.pl > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \ /build/cd-hit-4.8.1/cd-hit-para.pl > /build/cd-hit-4.8.1/debian/cd-hit/usr/share/man/man1//cd-hit-para.1 help2man --no-info --no-discard-stderr --version-string='4.8.1' \ --name='divide a FASTA file into pieces' \ /build/cd-hit-4.8.1/cd-hit-div.pl > /build/cd-hit-4.8.1/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='4.8.1' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \ # /build/cd-hit-4.8.1/psi-cd-hit.pl | \ # sed -e '/^Name "main::.*" used only once:/d' \ # > /build/cd-hit-4.8.1/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='4.8.1' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ # /build/cd-hit-4.8.1/psi-cd-hit-2d.pl > /build/cd-hit-4.8.1/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='4.8.1' \ # --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ # /build/cd-hit-4.8.1/psi-cd-hit-2d-g1.pl > /build/cd-hit-4.8.1/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-4.8.1' dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/cd-hit-4.8.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/cd-hit-4.8.1' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cd-hit' in '../cd-hit_4.8.1-4_amd64.deb'. dpkg-deb: building package 'cd-hit-dbgsym' in '../cd-hit-dbgsym_4.8.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cd-hit_4.8.1-4_amd64.buildinfo dpkg-genchanges --build=binary -O../cd-hit_4.8.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2885057 and its subdirectories I: Current time: Wed May 3 01:15:48 -12 2023 I: pbuilder-time-stamp: 1683119748 Wed May 3 13:15:49 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed May 3 13:15:49 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed May 3 13:16:39 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed May 3 13:16:39 UTC 2023 I: cd-hit_4.8.1-4_amd64.changes: Format: 1.8 Date: Fri, 20 Aug 2021 10:39:56 +0200 Source: cd-hit Binary: cd-hit cd-hit-dbgsym Architecture: amd64 Version: 4.8.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: cd-hit - suite of programs designed to quickly group sequences Closes: 992052 Changes: cd-hit (4.8.1-4) unstable; urgency=medium . * d/watch: fix broken link to github * d/control: add myself to uploaders * d/t/run-unit-test: disable memory limits in tests (Closes: #992052) * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 9a66bd8fa534076ca71cceaa5b7bf3cb91b32179 1988100 cd-hit-dbgsym_4.8.1-4_amd64.deb 973a5e0e61f10eb9c187ab90e7a99e8a70b6a0c2 5170 cd-hit_4.8.1-4_amd64.buildinfo af20e4d05f1ec06c6ac376d6d30b85618f822cc9 516380 cd-hit_4.8.1-4_amd64.deb Checksums-Sha256: c152ac2c9a5d32f14ec00abf0905b654ca39c9a10d89b4767d0bb3b012966899 1988100 cd-hit-dbgsym_4.8.1-4_amd64.deb fee8bb295150b90657e4d8c5af02f8c633a9ed9dcc0c266dfe0480cc9e96a4ff 5170 cd-hit_4.8.1-4_amd64.buildinfo 03ff42ee8562a5b0e7f068f47fcf353a2bfc7ec705268e622126612a72672b44 516380 cd-hit_4.8.1-4_amd64.deb Files: edb17e653480393f54ce3512ed584d1f 1988100 debug optional cd-hit-dbgsym_4.8.1-4_amd64.deb 27d96c32b33ad15e787bd0d6f2bb64b2 5170 science optional cd-hit_4.8.1-4_amd64.buildinfo baff0fdc9498625bc4ddd660a7720a41 516380 science optional cd-hit_4.8.1-4_amd64.deb Wed May 3 13:16:40 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/cd-hit_4.8.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/cd-hit_4.8.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/cd-hit_4.8.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/b1/cd-hit_4.8.1-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IhdQqEuf/b2/cd-hit_4.8.1-4_amd64.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: 0.326s) 0.326s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.041s) 0.040s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed May 3 13:16:41 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Wed May 3 13:16:41 UTC 2023 I: cd-hit from bookworm built successfully and reproducibly on amd64. Wed May 3 13:16:42 UTC 2023 I: Submitting .buildinfo files to external archives: Wed May 3 13:16:42 UTC 2023 I: Submitting 8.0K b1/cd-hit_4.8.1-4_amd64.buildinfo.asc Wed May 3 13:16:43 UTC 2023 I: Submitting 8.0K b2/cd-hit_4.8.1-4_amd64.buildinfo.asc Wed May 3 13:16:44 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 3 13:16:44 UTC 2023 I: Done submitting .buildinfo files. Wed May 3 13:16:44 UTC 2023 I: Removing signed cd-hit_4.8.1-4_amd64.buildinfo.asc files: removed './b1/cd-hit_4.8.1-4_amd64.buildinfo.asc' removed './b2/cd-hit_4.8.1-4_amd64.buildinfo.asc'