Running as unit: rb-build-arm64_10-88062.service ==================================================================================== Thu Jul 31 12:12:52 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_10) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Thu Jul 31 12:12:52 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-N1mv0jCE" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 12:12:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Jul 31 12:12:52 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-fOudQH' Thu Jul 31 12:12:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Thu Jul 31 12:12:53 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-cIuepF' ok, let's check if vcftools is building anywhere yet… ok, vcftools is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of vcftools in trixie on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Thu Jul 31 12:13:01 UTC 2025 I: starting to build vcftools/trixie/arm64 on jenkins on '2025-07-31 12:12' Thu Jul 31 12:13:01 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/88062/console.log 1753963981 arm64 trixie vcftools Thu Jul 31 12:13:01 UTC 2025 I: Downloading source for trixie/vcftools=0.1.16-3 --2025-07-31 12:13:01-- http://deb.debian.org/debian/pool/main/v/vcftools/vcftools_0.1.16-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2071 (2.0K) [text/prs.lines.tag] Saving to: ‘vcftools_0.1.16-3.dsc’ 0K .. 100% 125M=0s 2025-07-31 12:13:01 (125 MB/s) - ‘vcftools_0.1.16-3.dsc’ saved [2071/2071] --2025-07-31 12:13:01-- http://deb.debian.org/debian/pool/main/v/vcftools/vcftools_0.1.16-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2071 (2.0K) [text/prs.lines.tag] Saving to: ‘vcftools_0.1.16-3.dsc’ 0K .. 100% 125M=0s 2025-07-31 12:13:01 (125 MB/s) - ‘vcftools_0.1.16-3.dsc’ saved [2071/2071] Thu Jul 31 12:13:01 UTC 2025 I: vcftools_0.1.16-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vcftools Binary: vcftools Architecture: any Version: 0.1.16-3 Maintainer: Debian Med Packaging Team Uploaders: Thorsten Alteholz , Andreas Tille Homepage: https://vcftools.github.io/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/vcftools Vcs-Git: https://salsa.debian.org/med-team/vcftools.git Testsuite: autopkgtest Testsuite-Triggers: libtest-most-perl, tabix Build-Depends: debhelper-compat (= 13), pkg-config, zlib1g-dev Package-List: vcftools deb science optional arch=any Checksums-Sha1: f80b58da5ac19bbafb2404d4878374dcbd6c98a7 244585 vcftools_0.1.16.orig.tar.gz a4936e15f603f6444e37d0cd7048f96cea3a10d7 13968 vcftools_0.1.16-3.debian.tar.xz Checksums-Sha256: 8255da4c9627b63fa43a006234fb4a1d160c63207a3f6df68ff9149f50cfb81e 244585 vcftools_0.1.16.orig.tar.gz 45443fb86bc37c71fc7f4cf2137cef7656ea06d97fdd2cdb549c34555ec88919 13968 vcftools_0.1.16-3.debian.tar.xz Files: 4b96ec3a1dedeb879a71ecb0c4578548 244585 vcftools_0.1.16.orig.tar.gz 781ec5bc24d85bd9bd2142fabc25a799 13968 vcftools_0.1.16-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFejpYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGw2A//WYgC4unPNzKBrPLKIumdgdq/Fpp3MfKF qM0M/walrHRTRcMGd8F8WpGquu5Aeda0njVN9IQeKvNXVMaonOqx001OPwHz/RIP QJADPmgdaF9PK5k90L08WydhngNocq23LL9rTJIj8+DsBM2r5iy5BK9jYMM7YVhe r5ZJxxtsVVz2xsFe5dCp8In16jX5AN+4yNPo5L+Wsl6RjkPujzyVgjYOWSJwQjal CHDJP3+njSKw4fWHQK3+if9EF5OE4iDrYJYR1frY4VJpi0JgbasHx+24yBknPA/X O5hLxe7sy/ibIUQt8csTQFf0yNrEF9634TQLcQfxgk6+NQ95AqOot1jtfIdUb9+u WjQYLkCtmV0Wu/bQjSwjBOVXFE+yLHW+JRHUx63Lmbrqqt8vbY9F26W32JAqC7X0 EZhiCJvQiwrFc4P4GNaa7wOLRNSxj90C1xaK0oaboUeCY0V9xoEJb8sQGob2YdB4 7eTbWo9kjw6KPAUju87JtmdXJ3HcSbYQtIfJTXA2iInZSIj7D485T1hHEWK1bxm0 QsDOuGvEpf4+quL69/4gsm0e5bKtJaZ4vpKxZrKRJV7cmxfnpv3PIc8x9JapXGOg nXrzpQO6FrHF7CQkWwF36SGLD+dd9O2Y8gsGnDfoPmodWxyEaaCR96vv+vpm7R6R QQ4D9A1qLzA= =fhdb -----END PGP SIGNATURE----- Thu Jul 31 12:13:01 UTC 2025 I: Checking whether the package is not for us Thu Jul 31 12:13:01 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Jul 31 12:13:01 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Jul 31 12:13:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Jul 31 12:13:01 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-uzMYRM' ==================================================================================== Thu Jul 31 12:13:02 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 vcftools trixie /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E 0.1.16-3" as arguments. Thu Jul 31 12:13:02 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-QCzS3Jpu" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 12:13:02 UTC 2025 I: Downloading source for trixie/vcftools=0.1.16-3 Reading package lists... NOTICE: 'vcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vcftools.git Please use: git clone https://salsa.debian.org/med-team/vcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 261 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (dsc) [2071 B] Get:2 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (tar) [245 kB] Get:3 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (diff) [14.0 kB] Fetched 261 kB in 0s (1897 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'vcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vcftools.git Please use: git clone https://salsa.debian.org/med-team/vcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 261 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (dsc) [2071 B] Get:2 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (tar) [245 kB] Get:3 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (diff) [14.0 kB] Fetched 261 kB in 0s (1897 kB/s) Download complete and in download only mode ============================================================================= Building vcftools in trixie on arm64 on codethink04-arm64 now. Date: Thu Jul 31 13:13:03 BST 2025 Date UTC: Thu Jul 31 12:13:03 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 31 00:13:03 -12 2025 I: pbuilder-time-stamp: 1753963983 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [vcftools_0.1.16-3.dsc] I: copying [./vcftools_0.1.16.orig.tar.gz] I: copying [./vcftools_0.1.16-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found dpkg-source: info: extracting vcftools in vcftools-0.1.16 dpkg-source: info: unpacking vcftools_0.1.16.orig.tar.gz dpkg-source: info: unpacking vcftools_0.1.16-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying temporary_test_fix.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpage.patch dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b1a556ca863d458d8e88a564e5f72950' 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='673615' 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.0z3Zup5E/pbuilderrc_v3Yt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1 --logfile b1/build.log vcftools_0.1.16-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, 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 ... 19964 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 pkg-config; however: Package pkg-config 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{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, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 12.0 MB of archives. After unpacking 46.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 12.0 MB in 0s (125 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/vcftools-0.1.16/ && 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 > ../vcftools_0.1.16-3_source.changes dpkg-buildpackage: info: source package vcftools dpkg-buildpackage: info: source version 0.1.16-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/vcftools.substvars debian/files rm -fr -- debian/vcftools/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_configure -- --with-pmdir=/share/perl5 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/share/perl5 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for arpa/inet.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for netdb.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for int8_t... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for error_at_line... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... yes checking for memset... yes checking for pow... no checking for select... yes checking for socket... yes checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for strtol... yes 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 src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make all-recursive make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making all in src make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making all in cpp make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp bgzf.c: In function 'bgzf_check_EOF': bgzf.c:60:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgzf.c:622:9: note: in expansion of macro '_bgzf_read' 622 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp variant_file_filters.cpp: In member function 'void variant_file::filter_individuals_randomly(int)': variant_file_filters.cpp:129:23: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from variant_file.h:15, from variant_file_filters.cpp:7: /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/algorithm:60, from variant_file.h:15, from variant_file_output.cpp:8: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': variant_file_output.cpp:4426:39: required from here 4426 | p_emission[ui].push_back(make_pair(p_emission_given_auto, p_emission_given_nonauto)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making all in perl make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making check in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making check in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making check in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -fr -- /tmp/dh-xdg-rundir-WS3qY2Dw create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/vcftools.substvars rm -fr -- debian/.debhelper/generated/vcftools/ debian/vcftools/ debian/tmp/ dh_auto_install --destdir=debian/vcftools/ install -m0755 -d /build/reproducible-path/vcftools-0.1.16/debian/vcftools make -j12 install DESTDIR=/build/reproducible-path/vcftools-0.1.16/debian/vcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making install in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making install in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' /usr/bin/install -c vcftools '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 vcftools.1 '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making install in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' 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/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_install for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installdocs install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -m0755 -d debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/README.test debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/tests/run-unit-test debian/vcftools/usr/share/doc/vcftools chmod -R u\+rw,go=rX debian/vcftools/usr/share/doc install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright rm -f debian/vcftools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installchangelogs src/perl/ChangeLog install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -p -m0644 debian/.debhelper/generated/vcftools/dh_installchangelogs.dch.trimmed debian/vcftools/usr/share/doc/vcftools/changelog.Debian install -p -m0644 src/perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installexamples; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata; cp ./examples/* /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata/; find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \; sed -i 's#examples#testdata#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#I\.\./perl/#I\.\./\.#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#\.\./perl/#/usr/bin/#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; for perlscript in `grep -lR '#!/usr/bin/env \+perl' debian/*/usr/share/doc/vcftools/examples` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installman install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./src/cpp/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1 mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1 mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 dh_perl mv debian/vcftools.substvars.new debian/vcftools.substvars rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5 dh_link dh_strip_nondeterminism dh_compress cd debian/vcftools chmod a-x usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 gzip -9nf usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 cd '/build/reproducible-path/vcftools-0.1.16' dh_fixperms find debian/vcftools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/vcftools/usr/share/doc -type f -a -true -a ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/vcftools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a-X find debian/vcftools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/vcftools/usr/bin/vcftools dh_strip -a install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools objcopy --add-gnu-debuglink debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug debian/vcftools/usr/bin/vcftools install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/share/doc ln -s vcftools debian/.debhelper/vcftools/dbgsym-root/usr/share/doc/vcftools-dbgsym install -m0755 -d debian/.debhelper/vcftools dh_makeshlibs -a rm -f debian/vcftools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/vcftools/DEBIAN dpkg-shlibdeps -Tdebian/vcftools.substvars debian/vcftools/usr/bin/vcftools dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/vcftools/DEBIAN dh_gencontrol install -m0755 -d debian/vcftools/DEBIAN echo misc:Depends= >> debian/vcftools.substvars echo misc:Pre-Depends= >> debian/vcftools.substvars install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=e1ff97308716f24c6998640e23eecb0646991355 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/vcftools chmod 0644 -- debian/vcftools/DEBIAN/control dh_md5sums install -m0755 -d debian/vcftools/DEBIAN cd debian/vcftools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/vcftools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN cd debian/.debhelper/vcftools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/vcftools .. dpkg-deb --root-owner-group --build debian/.debhelper/vcftools/dbgsym-root .. dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-3_arm64.deb'. dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.16-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../vcftools_0.1.16-3_arm64.buildinfo dpkg-genchanges --build=binary -O../vcftools_0.1.16-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/673615 and its subdirectories I: Current time: Thu Jul 31 00:14:07 -12 2025 I: pbuilder-time-stamp: 1753964047 Thu Jul 31 12:14:07 UTC 2025 I: Signing ./b1/vcftools_0.1.16-3_arm64.buildinfo as vcftools_0.1.16-3_arm64.buildinfo.asc Thu Jul 31 12:14:07 UTC 2025 I: Signed ./b1/vcftools_0.1.16-3_arm64.buildinfo as ./b1/vcftools_0.1.16-3_arm64.buildinfo.asc Thu Jul 31 12:14:07 UTC 2025 - build #1 for vcftools/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Jul 31 12:14:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-QCzS3Jpu, removing. /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 12:14 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 12:13 b2 -rw------- 1 jenkins jenkins 3189 Jul 31 12:13 rbuildlog.WLGQRSJ -rw-r--r-- 1 jenkins jenkins 2071 Oct 7 2021 vcftools_0.1.16-3.dsc /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1: total 5420 -rw-r--r-- 1 jenkins jenkins 60605 Jul 31 12:14 build.log -rw-r--r-- 1 jenkins jenkins 5029960 Jul 31 12:14 vcftools-dbgsym_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 13968 Jul 31 12:14 vcftools_0.1.16-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2071 Jul 31 12:14 vcftools_0.1.16-3.dsc -rw-r--r-- 1 jenkins jenkins 5008 Jul 31 12:14 vcftools_0.1.16-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5890 Jul 31 12:14 vcftools_0.1.16-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1418 Jul 31 12:14 vcftools_0.1.16-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 407104 Jul 31 12:14 vcftools_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1279 Jul 31 12:14 vcftools_0.1.16-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2: total 0 Thu Jul 31 12:14:08 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 31 00:13:03 -12 2025 I: pbuilder-time-stamp: 1753963983 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [vcftools_0.1.16-3.dsc] I: copying [./vcftools_0.1.16.orig.tar.gz] I: copying [./vcftools_0.1.16-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found dpkg-source: info: extracting vcftools in vcftools-0.1.16 dpkg-source: info: unpacking vcftools_0.1.16.orig.tar.gz dpkg-source: info: unpacking vcftools_0.1.16-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying temporary_test_fix.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpage.patch dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b1a556ca863d458d8e88a564e5f72950' 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='673615' 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.0z3Zup5E/pbuilderrc_v3Yt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1 --logfile b1/build.log vcftools_0.1.16-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, 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 ... 19964 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 pkg-config; however: Package pkg-config 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{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, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 12.0 MB of archives. After unpacking 46.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 12.0 MB in 0s (125 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. 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Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../29-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../30-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../31-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../32-pkg-config_1.8.1-4_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../33-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... 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/reproducible-path/vcftools-0.1.16/ && 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 > ../vcftools_0.1.16-3_source.changes dpkg-buildpackage: info: source package vcftools dpkg-buildpackage: info: source version 0.1.16-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/vcftools.substvars debian/files rm -fr -- debian/vcftools/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_configure -- --with-pmdir=/share/perl5 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/share/perl5 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for arpa/inet.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for netdb.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for int8_t... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for error_at_line... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... yes checking for memset... yes checking for pow... no checking for select... yes checking for socket... yes checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for strtol... yes 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 src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make all-recursive make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making all in src make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making all in cpp make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp bgzf.c: In function 'bgzf_check_EOF': bgzf.c:60:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgzf.c:622:9: note: in expansion of macro '_bgzf_read' 622 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp variant_file_filters.cpp: In member function 'void variant_file::filter_individuals_randomly(int)': variant_file_filters.cpp:129:23: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from variant_file.h:15, from variant_file_filters.cpp:7: /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/algorithm:60, from variant_file.h:15, from variant_file_output.cpp:8: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': variant_file_output.cpp:4426:39: required from here 4426 | p_emission[ui].push_back(make_pair(p_emission_given_auto, p_emission_given_nonauto)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making all in perl make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making check in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making check in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making check in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -fr -- /tmp/dh-xdg-rundir-WS3qY2Dw create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/vcftools.substvars rm -fr -- debian/.debhelper/generated/vcftools/ debian/vcftools/ debian/tmp/ dh_auto_install --destdir=debian/vcftools/ install -m0755 -d /build/reproducible-path/vcftools-0.1.16/debian/vcftools make -j12 install DESTDIR=/build/reproducible-path/vcftools-0.1.16/debian/vcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making install in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making install in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' /usr/bin/install -c vcftools '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 vcftools.1 '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making install in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' 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/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_install for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installdocs install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -m0755 -d debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/README.test debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/tests/run-unit-test debian/vcftools/usr/share/doc/vcftools chmod -R u\+rw,go=rX debian/vcftools/usr/share/doc install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright rm -f debian/vcftools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installchangelogs src/perl/ChangeLog install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -p -m0644 debian/.debhelper/generated/vcftools/dh_installchangelogs.dch.trimmed debian/vcftools/usr/share/doc/vcftools/changelog.Debian install -p -m0644 src/perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installexamples; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata; cp ./examples/* /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata/; find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \; sed -i 's#examples#testdata#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#I\.\./perl/#I\.\./\.#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#\.\./perl/#/usr/bin/#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; for perlscript in `grep -lR '#!/usr/bin/env \+perl' debian/*/usr/share/doc/vcftools/examples` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installman install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./src/cpp/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1 mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1 mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 dh_perl mv debian/vcftools.substvars.new debian/vcftools.substvars rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5 dh_link dh_strip_nondeterminism dh_compress cd debian/vcftools chmod a-x usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 gzip -9nf usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 cd '/build/reproducible-path/vcftools-0.1.16' dh_fixperms find debian/vcftools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/vcftools/usr/share/doc -type f -a -true -a ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/vcftools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a-X find debian/vcftools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/vcftools/usr/bin/vcftools dh_strip -a install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools objcopy --add-gnu-debuglink debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug debian/vcftools/usr/bin/vcftools install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/share/doc ln -s vcftools debian/.debhelper/vcftools/dbgsym-root/usr/share/doc/vcftools-dbgsym install -m0755 -d debian/.debhelper/vcftools dh_makeshlibs -a rm -f debian/vcftools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/vcftools/DEBIAN dpkg-shlibdeps -Tdebian/vcftools.substvars debian/vcftools/usr/bin/vcftools dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/vcftools/DEBIAN dh_gencontrol install -m0755 -d debian/vcftools/DEBIAN echo misc:Depends= >> debian/vcftools.substvars echo misc:Pre-Depends= >> debian/vcftools.substvars install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=e1ff97308716f24c6998640e23eecb0646991355 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/vcftools chmod 0644 -- debian/vcftools/DEBIAN/control dh_md5sums install -m0755 -d debian/vcftools/DEBIAN cd debian/vcftools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/vcftools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN cd debian/.debhelper/vcftools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/vcftools .. dpkg-deb --root-owner-group --build debian/.debhelper/vcftools/dbgsym-root .. dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-3_arm64.deb'. dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.16-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../vcftools_0.1.16-3_arm64.buildinfo dpkg-genchanges --build=binary -O../vcftools_0.1.16-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/673615 and its subdirectories I: Current time: Thu Jul 31 00:14:07 -12 2025 I: pbuilder-time-stamp: 1753964047 Thu Jul 31 12:14:08 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Thu Jul 31 12:14:08 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Thu Jul 31 12:14:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Thu Jul 31 12:14:08 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-nB80yw' ==================================================================================== Wed Sep 2 18:37:10 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 vcftools trixie /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E 0.1.16-3" as arguments. Wed Sep 2 18:37:10 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-E5DMJTwN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 2 18:37:10 UTC 2026 I: Downloading source for trixie/vcftools=0.1.16-3 Reading package lists... NOTICE: 'vcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vcftools.git Please use: git clone https://salsa.debian.org/med-team/vcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 261 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (dsc) [2071 B] Get:2 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (tar) [245 kB] Get:3 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (diff) [14.0 kB] Fetched 261 kB in 0s (14.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'vcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vcftools.git Please use: git clone https://salsa.debian.org/med-team/vcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 261 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (dsc) [2071 B] Get:2 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (tar) [245 kB] Get:3 http://deb.debian.org/debian trixie/main vcftools 0.1.16-3 (diff) [14.0 kB] Fetched 261 kB in 0s (14.5 MB/s) Download complete and in download only mode ============================================================================= Re-Building vcftools in trixie on arm64 on codethink03-arm64 now. Date: Wed Sep 2 19:37:10 BST 2026 Date UTC: Wed Sep 2 18:37:10 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/pbuilderrc_Zuev + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' vcftools = debian-installer -o vcftools = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' vcftools = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/pbuilderrc_Zuev --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2 --logfile b2/build.log vcftools_0.1.16-3.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 3 08:37:10 +14 2026 I: pbuilder-time-stamp: 1788374230 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [vcftools_0.1.16-3.dsc] I: copying [./vcftools_0.1.16.orig.tar.gz] I: copying [./vcftools_0.1.16-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found dpkg-source: info: extracting vcftools in vcftools-0.1.16 dpkg-source: info: unpacking vcftools_0.1.16.orig.tar.gz dpkg-source: info: unpacking vcftools_0.1.16-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying temporary_test_fix.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpage.patch dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 2 18:37 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=094d620bf53942aab908d20d7c5a86b2 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=759723 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/pbuilderrc_Zuev --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2 --logfile b2/build.log vcftools_0.1.16-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, 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 ... 19964 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 pkg-config; however: Package pkg-config 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{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, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 12.0 MB of archives. After unpacking 46.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 12.0 MB in 0s (99.7 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../29-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../30-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../31-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../32-pkg-config_1.8.1-4_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../33-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... 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: user script /srv/workspace/pbuilder/759723/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/759723/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/vcftools-0.1.16/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../vcftools_0.1.16-3_source.changes dpkg-buildpackage: info: source package vcftools dpkg-buildpackage: info: source version 0.1.16-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/vcftools.substvars debian/files rm -fr -- debian/vcftools/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_configure -- --with-pmdir=/share/perl5 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/share/perl5 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 xargs -n works... 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for arpa/inet.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for netdb.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for int8_t... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for error_at_line... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... yes checking for memset... yes checking for pow... no checking for select... yes checking for socket... yes checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for strtol... yes 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 src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make all-recursive make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making all in src make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making all in cpp make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp bgzf.c: In function 'bgzf_check_EOF': bgzf.c:60:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgzf.c:622:9: note: in expansion of macro '_bgzf_read' 622 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp variant_file_filters.cpp: In member function 'void variant_file::filter_individuals_randomly(int)': variant_file_filters.cpp:129:23: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from variant_file.h:15, from variant_file_filters.cpp:7: /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/algorithm:60, from variant_file.h:15, from variant_file_output.cpp:8: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': variant_file_output.cpp:4426:39: required from here 4426 | p_emission[ui].push_back(make_pair(p_emission_given_auto, p_emission_given_nonauto)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making all in perl make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making check in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making check in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making check in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -fr -- /tmp/dh-xdg-rundir-RxcaktUn create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/vcftools.substvars rm -fr -- debian/.debhelper/generated/vcftools/ debian/vcftools/ debian/tmp/ dh_auto_install --destdir=debian/vcftools/ install -m0755 -d /build/reproducible-path/vcftools-0.1.16/debian/vcftools make -j12 install DESTDIR=/build/reproducible-path/vcftools-0.1.16/debian/vcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making install in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making install in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' /usr/bin/install -c vcftools '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 vcftools.1 '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making install in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' 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/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_install for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installdocs install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -m0755 -d debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/README.test debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/tests/run-unit-test debian/vcftools/usr/share/doc/vcftools chmod -R u\+rw,go=rX debian/vcftools/usr/share/doc install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright rm -f debian/vcftools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installchangelogs src/perl/ChangeLog install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -p -m0644 debian/.debhelper/generated/vcftools/dh_installchangelogs.dch.trimmed debian/vcftools/usr/share/doc/vcftools/changelog.Debian install -p -m0644 src/perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installexamples; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata; cp ./examples/* /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata/; find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \; sed -i 's#examples#testdata#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#I\.\./perl/#I\.\./\.#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#\.\./perl/#/usr/bin/#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; for perlscript in `grep -lR '#!/usr/bin/env \+perl' debian/*/usr/share/doc/vcftools/examples` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installman install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./src/cpp/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1 mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1 mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 dh_perl mv debian/vcftools.substvars.new debian/vcftools.substvars rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5 dh_link dh_strip_nondeterminism dh_compress cd debian/vcftools chmod a-x usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 gzip -9nf usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 cd '/build/reproducible-path/vcftools-0.1.16' dh_fixperms find debian/vcftools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/vcftools/usr/share/doc -type f -a -true -a ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/vcftools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a-X find debian/vcftools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/vcftools/usr/bin/vcftools dh_strip -a install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools objcopy --add-gnu-debuglink debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/e1/ff97308716f24c6998640e23eecb0646991355.debug debian/vcftools/usr/bin/vcftools install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/share/doc ln -s vcftools debian/.debhelper/vcftools/dbgsym-root/usr/share/doc/vcftools-dbgsym install -m0755 -d debian/.debhelper/vcftools dh_makeshlibs -a rm -f debian/vcftools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/vcftools/DEBIAN dpkg-shlibdeps -Tdebian/vcftools.substvars debian/vcftools/usr/bin/vcftools dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/vcftools/DEBIAN dh_gencontrol install -m0755 -d debian/vcftools/DEBIAN echo misc:Depends= >> debian/vcftools.substvars echo misc:Pre-Depends= >> debian/vcftools.substvars install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=e1ff97308716f24c6998640e23eecb0646991355 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/vcftools chmod 0644 -- debian/vcftools/DEBIAN/control dh_md5sums install -m0755 -d debian/vcftools/DEBIAN cd debian/vcftools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/vcftools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN cd debian/.debhelper/vcftools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/vcftools .. dpkg-deb --root-owner-group --build debian/.debhelper/vcftools/dbgsym-root .. dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-3_arm64.deb'. dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.16-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../vcftools_0.1.16-3_arm64.buildinfo dpkg-genchanges --build=binary -O../vcftools_0.1.16-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/759723/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/759723/tmp/hooks/B01_cleanup finished 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/759723 and its subdirectories I: Current time: Thu Sep 3 08:38:15 +14 2026 I: pbuilder-time-stamp: 1788374295 + false + set +x Wed Sep 2 18:38:15 UTC 2026 I: Signing ./b2/vcftools_0.1.16-3_arm64.buildinfo as vcftools_0.1.16-3_arm64.buildinfo.asc Wed Sep 2 18:38:15 UTC 2026 I: Signed ./b2/vcftools_0.1.16-3_arm64.buildinfo as ./b2/vcftools_0.1.16-3_arm64.buildinfo.asc Wed Sep 2 18:38:15 UTC 2026 - build #2 for vcftools/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Wed Sep 2 18:38:15 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-E5DMJTwN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E: total 80 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 12:14 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 12:15 b2 -rw------- 1 jenkins jenkins 64095 Jul 31 12:14 rbuildlog.WLGQRSJ -rw-r--r-- 1 jenkins jenkins 2071 Oct 7 2021 vcftools_0.1.16-3.dsc /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1: total 5440 -rw-r--r-- 1 jenkins jenkins 60605 Jul 31 12:14 build.log -rw-r--r-- 1 jenkins jenkins 5029960 Jul 31 12:14 vcftools-dbgsym_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 13968 Jul 31 12:14 vcftools_0.1.16-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2071 Jul 31 12:14 vcftools_0.1.16-3.dsc -rw-r--r-- 1 jenkins jenkins 5008 Jul 31 12:14 vcftools_0.1.16-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5890 Jul 31 12:14 vcftools_0.1.16-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1418 Jul 31 12:14 vcftools_0.1.16-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 407104 Jul 31 12:14 vcftools_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1279 Jul 31 12:14 vcftools_0.1.16-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2: total 5424 -rw-r--r-- 1 jenkins jenkins 62543 Jul 31 12:15 build.log -rw-r--r-- 1 jenkins jenkins 5029960 Jul 31 12:15 vcftools-dbgsym_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 13968 Jul 31 12:15 vcftools_0.1.16-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2071 Jul 31 12:15 vcftools_0.1.16-3.dsc -rw-r--r-- 1 jenkins jenkins 5008 Jul 31 12:15 vcftools_0.1.16-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5890 Jul 31 12:15 vcftools_0.1.16-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1418 Jul 31 12:15 vcftools_0.1.16-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 407104 Jul 31 12:15 vcftools_0.1.16-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1279 Jul 31 12:15 vcftools_0.1.16-3_source.changes Thu Jul 31 12:15:16 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Thu Jul 31 12:15:17 UTC 2025 I: vcftools_0.1.16-3_arm64.changes: Format: 1.8 Date: Thu, 07 Oct 2021 07:36:06 +0200 Source: vcftools Binary: vcftools vcftools-dbgsym Architecture: arm64 Version: 0.1.16-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: vcftools - Collection of tools to work with VCF files Changes: vcftools (0.1.16-3) unstable; urgency=medium . * Fix watchfile to detect new versions on github (routine-update) * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: cb16c702afee8489a4aabac4a94b4405d9acf416 5029960 vcftools-dbgsym_0.1.16-3_arm64.deb 3b8d8b005143ddbe989b00cdd94f6cfb492d288a 5008 vcftools_0.1.16-3_arm64.buildinfo c5c16b7a2ab99dfe430da21861b92ff00048cfb3 407104 vcftools_0.1.16-3_arm64.deb Checksums-Sha256: a584a85eb467bb2284bdcf5c04e50fde6a3fc209277f7e1b0a48ec45e492bf89 5029960 vcftools-dbgsym_0.1.16-3_arm64.deb eae884c94d51740aaeb0a55f7d3c3fe227b9b233835179e6d5bf924cbd7e35ac 5008 vcftools_0.1.16-3_arm64.buildinfo 500ec454f662a8cced16e095818298bcbe160b12e87d2fb48ab06a6c1e19bcb5 407104 vcftools_0.1.16-3_arm64.deb Files: f546c23ee340b21374d4a5ccf2899bb5 5029960 debug optional vcftools-dbgsym_0.1.16-3_arm64.deb e030bc6551ff204e7a0ed52950dd8e63 5008 science optional vcftools_0.1.16-3_arm64.buildinfo 39bb4e616a4fb40be6d5bc02a709563d 407104 science optional vcftools_0.1.16-3_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/vcftools_0.1.16-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/vcftools_0.1.16-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/vcftools_0.1.16-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/vcftools_0.1.16-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/vcftools_0.1.16-3_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/vcftools_0.1.16-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-07-31 12:14:07.935305286 +0000 +++ b2/build.log 2025-07-31 12:15:16.703398856 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 31 00:13:03 -12 2025 -I: pbuilder-time-stamp: 1753963983 +I: Current time: Thu Sep 3 08:37:10 +14 2026 +I: pbuilder-time-stamp: 1788374230 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 2 18:37 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b1a556ca863d458d8e88a564e5f72950' - 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='673615' - PS1='# ' - PS2='> ' + INVOCATION_ID=094d620bf53942aab908d20d7c5a86b2 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=759723 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.0z3Zup5E/pbuilderrc_v3Yt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1 --logfile b1/build.log vcftools_0.1.16-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/pbuilderrc_Zuev --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2 --logfile b2/build.log vcftools_0.1.16-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/673615/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 32 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 12.0 MB in 0s (125 MB/s) +Fetched 12.0 MB in 0s (99.7 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) @@ -297,7 +329,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/vcftools-0.1.16/ && 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 > ../vcftools_0.1.16-3_source.changes +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/vcftools-0.1.16/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../vcftools_0.1.16-3_source.changes dpkg-buildpackage: info: source package vcftools dpkg-buildpackage: info: source version 0.1.16-3 dpkg-buildpackage: info: source distribution unstable @@ -478,7 +514,6 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp variant_file_filters.cpp: In member function 'void variant_file::filter_individuals_randomly(int)': variant_file_filters.cpp:129:23: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order @@ -489,10 +524,9 @@ /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/algorithm:60, from variant_file.h:15, @@ -504,6 +538,8 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making all in perl @@ -538,7 +574,7 @@ make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' - rm -fr -- /tmp/dh-xdg-rundir-WS3qY2Dw + rm -fr -- /tmp/dh-xdg-rundir-RxcaktUn create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/vcftools.substvars @@ -677,45 +713,45 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 - mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 - mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 - mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 - mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 - mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 - mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 - mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 - mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 - mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 - mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 - mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1 mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 - mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 - mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 - mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 + mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 + mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 + mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 + mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 + mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1 + mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 + mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 + mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1 mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 + mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 + mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 + mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 + mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 + mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 + mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 - mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 - mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 - mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 - chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 + mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 + mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 + mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 + chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 dh_perl mv debian/vcftools.substvars.new debian/vcftools.substvars rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5 @@ -785,12 +821,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/759723/tmp/hooks/B01_cleanup finished 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/673615 and its subdirectories -I: Current time: Thu Jul 31 00:14:07 -12 2025 -I: pbuilder-time-stamp: 1753964047 +I: removing directory /srv/workspace/pbuilder/759723 and its subdirectories +I: Current time: Thu Sep 3 08:38:15 +14 2026 +I: pbuilder-time-stamp: 1788374295 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/vcftools_0.1.16-3.diff: 79.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/vcftools_0.1.16-3.diff.gz b2/build.log: 81.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.2% -- replaced with stdout Thu Jul 31 12:15:18 UTC 2025 I: diffoscope 302 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_vcftools_trixie_arm64_1753964118 + touch /var/log/reproducible-builds/diffoscope_stamp_vcftools_trixie_arm64_1753964118 + RESULT=0 + systemd-run '--description=diffoscope on vcftools/0.1.16-3 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_10-88062 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E --run-session -c jenkins-reproducible-trixie-diffoscope-8fe96621-e0b6-4eef-9764-2ecc9199c7fd -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/dbd-tmp-yDBzbR1 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1/vcftools_0.1.16-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2/vcftools_0.1.16-3_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_10-88062.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/vcftools_0.1.16-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b1/vcftools_0.1.16-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0z3Zup5E/b2/vcftools_0.1.16-3_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 157ms CPU time consumed: 158ms __ _ _ __ _____ / _| |_ ___ ___ | |___ \ \ / / __| |_| __/ _ \ / _ \| / __| \ V / (__| _| || (_) | (_) | \__ \ \_/ \___|_| \__\___/ \___/|_|___/ Thu Jul 31 12:15:18 UTC 2025 I: diffoscope 302 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 31 12:15:18 UTC 2025 I: vcftools from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-07-31 12:15:19] INFO: Starting at 2025-07-31 12:15:19.075014 [2025-07-31 12:15:19] INFO: Generating the pages of 1 package(s) [2025-07-31 12:15:19] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/vcftools didn't produce a buildlog, even though it has been built. [2025-07-31 12:15:19] INFO: Finished at 2025-07-31 12:15:19.306346, took: 0:00:00.231337 Thu Jul 31 12:15:19 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/vcftools.html Thu Jul 31 12:15:19 UTC 2025 I: Removing signed vcftools_0.1.16-3_arm64.buildinfo.asc files: removed './b1/vcftools_0.1.16-3_arm64.buildinfo.asc' removed './b2/vcftools_0.1.16-3_arm64.buildinfo.asc' 1753964119 arm64 trixie vcftools Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/vcftools_0.1.16-3.rbuild.log: 79.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/vcftools_0.1.16-3.rbuild.log.gz [2025-07-31 12:15:19] INFO: Starting at 2025-07-31 12:15:19.564259 [2025-07-31 12:15:19] INFO: Generating the pages of 1 package(s) [2025-07-31 12:15:19] INFO: Finished at 2025-07-31 12:15:19.785669, took: 0:00:00.221415 All cleanup done. Thu Jul 31 12:15:19 UTC 2025 - total duration: 0h 2m 26s. Thu Jul 31 12:15:19 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-N1mv0jCE, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 27.368s CPU time consumed: 4.541s