Sun Feb 23 13:43:12 UTC 2025 I: starting to build minimac4/trixie/amd64 on jenkins on '2025-02-23 13:42' Sun Feb 23 13:43:12 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/51787/console.log Sun Feb 23 13:43:12 UTC 2025 I: Downloading source for trixie/minimac4=4.1.6-1 --2025-02-23 13:43:12-- http://deb.debian.org/debian/pool/main/m/minimac4/minimac4_4.1.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2288 (2.2K) [text/prs.lines.tag] Saving to: ‘minimac4_4.1.6-1.dsc’ 0K .. 100% 379M=0s 2025-02-23 13:43:12 (379 MB/s) - ‘minimac4_4.1.6-1.dsc’ saved [2288/2288] Sun Feb 23 13:43:12 UTC 2025 I: minimac4_4.1.6-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimac4 Binary: minimac4 Architecture: any Version: 4.1.6-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi , Étienne Mollier Homepage: https://genome.sph.umich.edu/wiki/Minimac4 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimac4 Vcs-Git: https://salsa.debian.org/med-team/minimac4.git Testsuite: autopkgtest Testsuite-Triggers: bcftools Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools Package-List: minimac4 deb science optional arch=any Checksums-Sha1: 190a527edb4cf800a0c3b6ed2cc732442c10ef72 53460 minimac4_4.1.6.orig.tar.gz 8104bc421b8d4b717ca4608f39775675dda37d23 5368 minimac4_4.1.6-1.debian.tar.xz Checksums-Sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333 53460 minimac4_4.1.6.orig.tar.gz 994819c4e4ff50247f6f7420ed438e7cd802baaa445beecf3f581ef8ef346b2c 5368 minimac4_4.1.6-1.debian.tar.xz Files: e7c0cfe90add2248fc79824add76253a 53460 minimac4_4.1.6.orig.tar.gz 86de610bf26bb05bae065ea9149df3d1 5368 minimac4_4.1.6-1.debian.tar.xz Dgit: f06073708f98230727f744ec1f0ae2b7a82b38c1 debian archive/debian/4.1.6-1 https://git.dgit.debian.org/minimac4 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVzCnkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoxww//VN8VG/iYLukZlL/mut4jDnSvmKn7 HZGN2OojXPMtzVlI7yCROdWICQXaNkzntWKNoP6fc5c6X15lrANtWNziLVHw3fKa RVnN8Z9uEL6QHVHPh+zfXa6sje4nrMiU7Fr5biaXCyeUS0ht30nX/M3L695CQF7b SppP3j4AX0gPpFaj8k/6onJZPbGaNIDj/sTgl67DLsE8k6ht9GJtvyuJs3IGbLg5 ZndqE3I1UQdSzwHs7SXia+kimXN848bUEBfoNi/FBBEpAX11eAEoX75ShKuLcjTW v6mXVQBoUZ99C6oOlqSHLTmPoOD/CuDab8YfIM4OIf7dpcjSdXEL/xQ5TGjnoMGn ncSsDMNqL+fNjWrYN/8LN5YTewK6g5qwxEtpAARdTu6NYfzWW9p2LT6Th+VNvk+o hY8SeYQGNqeOKjcRRD2V1RpRmc5mrq2eAcQ6gIYs0zypq4fozM1rqmcIIKYecago wFtcjn0VEGrPC6PhYjXAAS3DOeBWlRT2luw5mM6uu4zBSyTkpu4EdT4kTemUqO8+ f8mFIZ6fPER9n9Rer50I3IFSVkxn1mb2kHv76jJ1FiOHI7Q9WDEo5h2oiSdSjrZ/ iLAjZHB/Buu9O3cwlnVC6Xz6JxZtmhdp14kaLPkfF1c2Qo+T7MLMNd9uayUJM9b2 qrkjd+gngOl7TF8= =Hdso -----END PGP SIGNATURE----- Sun Feb 23 13:43:12 UTC 2025 I: Checking whether the package is not for us Sun Feb 23 13:43:12 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Sun Feb 23 13:43:12 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Sun Feb 23 13:44:44 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 23 01:43:14 -12 2025 I: pbuilder-time-stamp: 1740318194 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 [minimac4_4.1.6-1.dsc] I: copying [./minimac4_4.1.6.orig.tar.gz] I: copying [./minimac4_4.1.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./minimac4_4.1.6-1.dsc: unsupported subcommand dpkg-source: info: extracting minimac4 in minimac4-4.1.6 dpkg-source: info: unpacking minimac4_4.1.6.orig.tar.gz dpkg-source: info: unpacking minimac4_4.1.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Use_shared_zlib.patch dpkg-source: info: applying lzma.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/68447/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='cc5c9d6e4cef4ff4b413b7267760bcce' 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='68447' 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.JpyzneAI/pbuilderrc_ckG9 --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.JpyzneAI/b1 --logfile b1/build.log minimac4_4.1.6-1.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' I: uname -a Linux infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/68447/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libstatgen-dev, libshrinkwrap-dev, libsavvy-dev, libomp-jonathonl-dev, liblzma-dev, libzstd-dev, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19805 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libstatgen-dev; however: Package libstatgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libshrinkwrap-dev; however: Package libshrinkwrap-dev is not installed. pbuilder-satisfydepends-dummy depends on libsavvy-dev; however: Package libsavvy-dev is not installed. pbuilder-satisfydepends-dummy depends on libomp-jonathonl-dev; however: Package libomp-jonathonl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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} bcftools{a} bsdextrautils{a} cmake{a} cmake-data{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} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libomp-jonathonl-dev{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsavvy-dev{a} libshrinkwrap-dev{a} libssh2-1t64{a} libstatgen-dev{a} libstatgen1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-gffutils python3-matplotlib wget 0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 161 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 29 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.21-1 [784 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.5-2 [2267 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.5-2 [12.0 MB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libomp-jonathonl-dev amd64 1.0.0-1 [7816 B] Get: 70 http://deb.debian.org/debian trixie/main amd64 libshrinkwrap-dev all 1.2.0-2 [12.3 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libsavvy-dev all 2.1.0-3 [73.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libstatgen1 amd64 1.0.15-8 [316 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libstatgen-dev amd64 1.0.15-8 [122 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 44.7 MB in 3s (14.3 MB/s) Preconfiguring packages ... 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Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libshrinkwrap-dev (1.2.0-2) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libstatgen-dev:amd64 (1.0.15-8) ... Setting up cmake-data (3.31.5-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libomp-jonathonl-dev (1.0.0-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up automake (1:1.17-3) ... 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 (0.23.1-1) ... Setting up libsavvy-dev (2.1.0-3) ... Setting up libtool (2.5.4-3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up cmake (3.31.5-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up bcftools (1.21-1) ... Processing triggers for libc-bin (2.40-7) ... 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/minimac4-4.1.6/ && 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 > ../minimac4_4.1.6-1_source.changes dpkg-buildpackage: info: source package minimac4 dpkg-buildpackage: info: source version 4.1.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_configure -- -DBUILD_TESTS=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTS=ON .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make -f 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42%] Building CXX object CMakeFiles/minimac4.dir/src/input_prep.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -MF CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o.d -o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/hidden_markov_model.cpp [ 57%] Building CXX object CMakeFiles/minimac4.dir/src/recombination.cpp.o /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/recombination.cpp.o -MF CMakeFiles/minimac4.dir/src/recombination.cpp.o.d -o CMakeFiles/minimac4.dir/src/recombination.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/recombination.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/main.cpp.o -MF CMakeFiles/minimac4.dir/src/main.cpp.o.d -o CMakeFiles/minimac4.dir/src/main.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/main.cpp /usr/bin/c++ -DSAVVY_VERSION=\"2.1.0\" -DVERSION=\"4.1.6\" -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -std=gnu++11 -MD -MT CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -MF CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o.d -o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o -c /build/reproducible-path/minimac4-4.1.6/src/unique_haplotype.cpp [100%] Linking CXX executable minimac4 /usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/minimac4-4.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/minimac4.dir/link.d CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o CMakeFiles/minimac4.dir/src/hidden_markov_model.cpp.o CMakeFiles/minimac4.dir/src/input_prep.cpp.o CMakeFiles/minimac4.dir/src/recombination.cpp.o CMakeFiles/minimac4.dir/src/unique_haplotype.cpp.o CMakeFiles/minimac4.dir/src/main.cpp.o -o minimac4 -Wl,-Bstatic -lomp -Wl,-Bdynamic -llzma -lzstd -lz make[3]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' [100%] Built target minimac4 make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: simple_test 1: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_simple_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel.vcf" 1: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: haploid_and_diploid_test 2: Test command: /build/reproducible-path/minimac4-4.1.6/test/simple-test.sh "/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu/minimac4" "m4_haploid_and_diploid_test_output" "/build/reproducible-path/minimac4-4.1.6/test/input/ref_panel_with_haploid_sample.vcf" "/build/reproducible-path/minimac4-4.1.6/test/input/tar_panel_with_haploid_sample.vcf" 2: Working Directory: /build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 1: /usr/bin/bcftools 2: /usr/bin/bcftools 1: minimac v4.1.6 1: 2: minimac v4.1.6 2: 2: Mean Compression Ratio: 0.770455 2: Min Compression Ratio: 0.590909 2: Max Compression Ratio: 0.95 1: Mean Compression Ratio: 0.820455 1: Min Compression Ratio: 0.590909 1: Max Compression Ratio: 1.05 2: minimac v4.1.6 2: 2: Imputing chr20:1-10009927 ... 2: Loading target haplotypes ... 2: Loading target haplotypes took 0 seconds 2: Loading reference haplotypes ... 2: Loading reference haplotypes took 0 seconds 2: Typed sites to imputed sites ratio: 0.903226 (28/31) 2: Running HMM with 1 threads ... 1: minimac v4.1.6 1: 2: Completed 2 of 5 samples 1: Imputing chr20:1-10009927 ... 1: Loading target haplotypes ... 1: Loading target haplotypes took 0 seconds 1: Loading reference haplotypes ... 2: Completed 4 of 5 samples 1: Loading reference haplotypes took 0 seconds 1: Typed sites to imputed sites ratio: 0.903226 (28/31) 1: Running HMM with 1 threads ... 2: Completed 5 of 5 samples 2: Running HMM took 0 seconds 2: Writing temp files took 0 seconds 2: Merging temp files ... 2: Merging temp files took 0 seconds 2: 1: Completed 2 of 5 samples 2: Mean ER2: 1 2: 2: Total time for parsing input: 0 seconds 2: Total time for HMM: 0 seconds 2: Total time for writing output: 0 seconds 2: Total wall time (h:mm:ss): 0:00:00 1: Completed 4 of 5 samples 1: Completed 5 of 5 samples 1: Running HMM took 0 seconds 1: Writing temp files took 0 seconds 1: Merging temp files ... 1: Merging temp files took 0 seconds 1: 1/2 Test #2: haploid_and_diploid_test ......... Passed 0.68 sec 1: Mean ER2: 1 1 1: 1: Total time for parsing input: 0 seconds 1: Total time for HMM: 0 seconds 1: Total time for writing output: 0 seconds 1: Total wall time (h:mm:ss): 0:00:00 2/2 Test #1: simple_test ...................... Passed 0.69 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.69 sec make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/minimac4/ cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/minimac4-4.1.6/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/minimac4-4.1.6 -B/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/minimac4-4.1.6/debian/minimac4/usr/bin/minimac4 make[1]: Leaving directory '/build/reproducible-path/minimac4-4.1.6/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_4.1.6-1_amd64.deb'. dpkg-deb: building package 'minimac4' in '../minimac4_4.1.6-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimac4_4.1.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimac4_4.1.6-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/68447 and its subdirectories I: Current time: Sun Feb 23 01:44:43 -12 2025 I: pbuilder-time-stamp: 1740318283 Sun Feb 23 13:44:44 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Sun Feb 23 13:44:44 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Sun Feb 23 13:46:24 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Sun Feb 23 13:46:24 UTC 2025 I: minimac4_4.1.6-1_amd64.changes: Format: 1.8 Date: Fri, 08 Dec 2023 13:14:00 +0100 Source: minimac4 Binary: minimac4 minimac4-dbgsym Architecture: amd64 Version: 4.1.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: minimac4 - Fast Imputation Based on State Space Reduction HMM Changes: minimac4 (4.1.6-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 9d342303d772e03f2b8b1fbf5f63f494e53abc13 5691012 minimac4-dbgsym_4.1.6-1_amd64.deb d3397a7b7ed6f93cea0176fa35e55553d441a459 6338 minimac4_4.1.6-1_amd64.buildinfo f41d8ff465fadc3f7f60aedc7bbac0efcb89a4ef 261480 minimac4_4.1.6-1_amd64.deb Checksums-Sha256: 3b7d9272de67f9d41f3803d4b00e20c480a43ff26b8decfc24d200f1ed6dd13f 5691012 minimac4-dbgsym_4.1.6-1_amd64.deb 5ed06175dcadd49adcc0fff8a46dcddf7d991699665c8d00712d9f76081df745 6338 minimac4_4.1.6-1_amd64.buildinfo 12768f8320932897db0c048962550b6c1a67af137893d45112c27b16a6cb5471 261480 minimac4_4.1.6-1_amd64.deb Files: bcd648180be606a703c25a57ca5057cd 5691012 debug optional minimac4-dbgsym_4.1.6-1_amd64.deb a5929fec1f57fc9156622e1f9c14270d 6338 science optional minimac4_4.1.6-1_amd64.buildinfo 016c5c4918cf401ac755ea152e4571bb 261480 science optional minimac4_4.1.6-1_amd64.deb Sun Feb 23 13:46:25 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_37-51787.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.JpyzneAI/minimac4_4.1.6-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.JpyzneAI/minimac4_4.1.6-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.JpyzneAI/minimac4_4.1.6-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.JpyzneAI/b1/minimac4_4.1.6-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.JpyzneAI/b2/minimac4_4.1.6-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call 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: 242ms CPU time consumed: 237ms Sun Feb 23 13:46:26 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sun Feb 23 13:46:26 UTC 2025 I: minimac4 from trixie built successfully and reproducibly on amd64. Sun Feb 23 13:46:28 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Feb 23 13:46:28 UTC 2025 I: Submitting 8.0K b1/minimac4_4.1.6-1_amd64.buildinfo.asc Sun Feb 23 13:46:31 UTC 2025 I: Submitting 8.0K b2/minimac4_4.1.6-1_amd64.buildinfo.asc Sun Feb 23 13:46:33 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Feb 23 13:46:33 UTC 2025 I: Done submitting .buildinfo files. Sun Feb 23 13:46:33 UTC 2025 I: Removing signed minimac4_4.1.6-1_amd64.buildinfo.asc files: removed './b1/minimac4_4.1.6-1_amd64.buildinfo.asc' removed './b2/minimac4_4.1.6-1_amd64.buildinfo.asc'