Tue Dec 17 21:51:17 UTC 2024 I: starting to build snp-sites/trixie/armhf on jenkins on '2024-12-17 21:51' Tue Dec 17 21:51:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/14002/console.log Tue Dec 17 21:51:17 UTC 2024 I: Downloading source for trixie/snp-sites=2.5.1-2 --2024-12-17 21:51:17-- http://deb.debian.org/debian/pool/main/s/snp-sites/snp-sites_2.5.1-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2297 (2.2K) [text/prs.lines.tag] Saving to: ‘snp-sites_2.5.1-2.dsc’ 0K .. 100% 312M=0s 2024-12-17 21:51:17 (312 MB/s) - ‘snp-sites_2.5.1-2.dsc’ saved [2297/2297] Tue Dec 17 21:51:17 UTC 2024 I: snp-sites_2.5.1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snp-sites Binary: snp-sites, libsnp-sites1, libsnp-sites1-dev Architecture: any Version: 2.5.1-2 Maintainer: Debian Med Packaging Team Uploaders: Jorge Soares , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/snp-sites Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/snp-sites Vcs-Git: https://salsa.debian.org/med-team/snp-sites.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, zlib1g, zlib1g-dev Build-Depends: debhelper-compat (= 13), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor Package-List: libsnp-sites1 deb libs optional arch=any libsnp-sites1-dev deb libdevel optional arch=any snp-sites deb science optional arch=any Checksums-Sha1: 225ae5918875829a3d9d7a08daf383195d4edbe4 15577807 snp-sites_2.5.1.orig.tar.gz 12af4e31d7af55cbd45a81544e38654f21d7b8df 8252 snp-sites_2.5.1-2.debian.tar.xz Checksums-Sha256: 913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e 15577807 snp-sites_2.5.1.orig.tar.gz 711f075ad6b75b0ab8a61398a86f493cd3aa2c7391d8235d99b43d886a998e61 8252 snp-sites_2.5.1-2.debian.tar.xz Files: a4183dadd8f8d56398654c943e4f1811 15577807 snp-sites_2.5.1.orig.tar.gz 1783af829c28ebaa6dc0877b5c9953ca 8252 snp-sites_2.5.1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFXGQQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGvYg/8DMzTvRxsoVLdZAPcDHnwfQcsd0kyRYjq FYkD0E4+YAzG/vEqxLjAR6APJ+7eAKd7bAxFpf+vGC3/M9JZmFSukfzxYK9IGNQg cnz4g59Ta/RP0ywKriTBW5zQ3xV6oXSCs6p/LIvD2o4K8kvjMTHlEMp2vBS8H8Us qyHGSVkYFR0NueqX4pvS2IhAvGId8XvZvg0X62IawbEBoZwP9a1p52sRbykFZxSP hRZsaNiI8vfXchVttjEoXRzRj49pdxnZ6sFltiW1WnvAame3altcIcuq/sAYEqOn 2saHp0bwETWRErF3RyfABWCA5HTJx4MhksIp45vN5RQODL00mCAXlCxXMjfvt1Bc e+mDxo42X6C+51gqiIEJBg6WVtIJVEXwSQ8QpQuJdz2/FpIobRftBBb3V1xWZnE1 76p3wbkkU0o7d4n+VRPYq1Iv6w8Xq44g7hTFBhVuP3lQbeZazpueN2sWEo9yAvph KbaW6ncQDLPCMIBAFzTHiH/mG8R7j2yK8d/d+w2Z33NX14Tdjq7mP9DxcJTNsfKE mo7BNygntgUA5ipQnL3BkLgPB5c/pc0AsXwpU3+MnJn4nfkIQPi87qVruri00Shu 4HuehmtNmzfZXJRpmd8TMqm5lExPoewOahxgvt6J6DGBqs6Z1VrVHjrB3XzOOLLk b5Y88DuOC+E= =SxHM -----END PGP SIGNATURE----- Tue Dec 17 21:51:17 UTC 2024 I: Checking whether the package is not for us Tue Dec 17 21:51:17 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Tue Dec 17 21:51:17 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Tue Dec 17 21:53:20 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 17 09:51:28 -12 2024 I: pbuilder-time-stamp: 1734472288 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 [snp-sites_2.5.1-2.dsc] I: copying [./snp-sites_2.5.1.orig.tar.gz] I: copying [./snp-sites_2.5.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 1 14:19:48 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snp-sites_2.5.1-2.dsc: no acceptable signature found dpkg-source: info: extracting snp-sites in snp-sites-2.5.1 dpkg-source: info: unpacking snp-sites_2.5.1.orig.tar.gz dpkg-source: info: unpacking snp-sites_2.5.1-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/28733/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='3399ed59291a4547ac67a1b10155c7c4' 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='28733' 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.OKwz6zqu/pbuilderrc_Yz7n --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.OKwz6zqu/b1 --logfile b1/build.log snp-sites_2.5.1-2.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/28733/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: armhf 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), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19674 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} d-shlibs{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} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libpkgconf3{a} libruby{a} libruby3.1t64{a} libsubunit-dev{a} libsubunit0{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 28.5 MB of archives. After unpacking 102 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-2 [1348 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-6 [1091 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf rubygems-integration all 1.18 [6704 B] Get: 14 http://deb.debian.org/debian trixie/main armhf rake all 13.2.1-1 [65.2 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 19 http://deb.debian.org/debian trixie/main armhf ruby-sdbm armhf 1.0.0-5+b5 [13.3 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20240808-1 [77.9 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-1+b2 [45.4 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libruby3.1t64 armhf 3.1.2-8.4 [5081 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf ruby3.1 armhf 3.1.2-8.4 [664 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 27 http://deb.debian.org/debian trixie/main armhf ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf asciidoctor all 2.0.23-1 [88.7 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libsubunit0 armhf 1.4.2-3+b1 [6196 B] Get: 35 http://deb.debian.org/debian trixie/main armhf libsubunit-dev armhf 1.4.2-3+b1 [7336 B] Get: 36 http://deb.debian.org/debian trixie/main armhf check armhf 0.15.2-2+b1 [109 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf d-shlibs all 0.108 [11.0 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-4 [14.0 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Fetched 28.5 MB in 1s (34.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19674 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.3.2-2_armhf.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-6_armhf.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-12_armhf.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../12-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../13-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../14-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../15-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../16-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../17-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../18-ruby-sdbm_1.0.0-5+b5_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b5) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../19-libedit2_3.1-20240808-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20240808-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../20-libncurses6_6.5-2+b1_armhf.deb ... Unpacking libncurses6:armhf (6.5-2+b1) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../21-libyaml-0-2_0.2.5-1+b2_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1+b2) ... Selecting previously unselected package libruby3.1t64:armhf. Preparing to unpack .../22-libruby3.1t64_3.1.2-8.4_armhf.deb ... Unpacking libruby3.1t64:armhf (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../23-ruby3.1_3.1.2-8.4_armhf.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../24-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../25-ruby_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../26-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../27-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../28-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../29-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../30-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../31-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../32-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libsubunit0:armhf. Preparing to unpack .../33-libsubunit0_1.4.2-3+b1_armhf.deb ... Unpacking libsubunit0:armhf (1.4.2-3+b1) ... Selecting previously unselected package libsubunit-dev:armhf. Preparing to unpack .../34-libsubunit-dev_1.4.2-3+b1_armhf.deb ... Unpacking libsubunit-dev:armhf (1.4.2-3+b1) ... Selecting previously unselected package check:armhf. Preparing to unpack .../35-check_0.15.2-2+b1_armhf.deb ... Unpacking check:armhf (0.15.2-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../36-d-shlibs_0.108_all.deb ... Unpacking d-shlibs (0.108) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../37-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../38-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../39-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../40-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 .../41-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../42-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../43-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../44-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../45-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../46-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../47-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../48-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 .../49-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../50-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../51-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../52-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../53-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package pkg-config:armhf. Preparing to unpack .../54-pkg-config_1.8.1-4_armhf.deb ... Unpacking pkg-config:armhf (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../55-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1+b2) ... Setting up libdebhelper-perl (13.20) ... Setting up libedit2:armhf (3.1-20240808-1) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libsubunit0:armhf (1.4.2-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libncurses6:armhf (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.108) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up openssl (3.3.2-2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libsubunit-dev:armhf (1.4.2-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up check:armhf (0.15.2-2+b1) ... Setting up pkg-config:armhf (1.8.1-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Setting up rake (13.2.1-1) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up libruby3.1t64:armhf (3.1.2-8.4) ... Setting up libruby:armhf (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up ruby-sdbm:armhf (1.0.0-5+b5) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/snp-sites-2.5.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snp-sites_2.5.1-2_source.changes dpkg-buildpackage: info: source package snp-sites dpkg-buildpackage: info: source version 2.5.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:16: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:16: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... m4/m4_ax_check_zlib.m4:68: AX_CHECK_ZLIB is expanded from... configure.ac:16: the top level configure.ac:18: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:18: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:18: the top level configure.ac:14: installing './compile' configure.ac:7: installing './config.guess' configure.ac:7: installing './config.sub' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c 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 build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for check >= 0.8.2... yes checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc 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 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 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 zlib.h... yes checking for math.h... yes checking for getopt.h... yes checking for floor in -lm... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ 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 dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' Making all in src make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include --std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o snp_sites-main.o `test -f 'main.c' || echo './'`main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alignment-file.lo alignment-file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcf.lo vcf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignment-file.c -fPIC -DPIC -o .libs/alignment-file.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o vcf.c: In function 'format_allele_index': vcf.c:176:50: warning: '%i' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 176 | sprintf(result, "%i", index); | ^~ vcf.c:176:49: note: directive argument in the range [1, 2147483645] 176 | sprintf(result, "%i", index); | ^~~~ In file included from /usr/include/stdio.h:970, from vcf.c:22: In function 'sprintf', inlined from 'format_allele_index' at vcf.c:176:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylib-of-snp-sites.c -fPIC -DPIC -o .libs/phylib-of-snp-sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o snp-sites.lo snp-sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignment-file.c -o alignment-file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c snp-sites.c -fPIC -DPIC -o .libs/snp-sites.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fasta-of-snp-sites.lo fasta-of-snp-sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c fasta-of-snp-sites.c -fPIC -DPIC -o .libs/fasta-of-snp-sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c snp-sites.c -o snp-sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c fasta-of-snp-sites.c -o fasta-of-snp-sites.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 1:0 -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o libsnp-sites.la -rpath /usr/lib/arm-linux-gnueabihf alignment-file.lo vcf.lo phylib-of-snp-sites.lo snp-sites.lo fasta-of-snp-sites.lo -lz -lm libtool: link: gcc -shared -fPIC -DPIC .libs/alignment-file.o .libs/vcf.o .libs/phylib-of-snp-sites.o .libs/snp-sites.o .libs/fasta-of-snp-sites.o -L/usr/lib -lz -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsnp-sites.so.1 -o .libs/libsnp-sites.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libsnp-sites.so.1" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so.1") libtool: link: (cd ".libs" && rm -f "libsnp-sites.so" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so") libtool: link: ar cr .libs/libsnp-sites.a alignment-file.o vcf.o phylib-of-snp-sites.o snp-sites.o fasta-of-snp-sites.o libtool: link: ranlib .libs/libsnp-sites.a libtool: link: ( cd ".libs" && rm -f "libsnp-sites.la" && ln -s "../libsnp-sites.la" "libsnp-sites.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc --std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o snp-sites snp_sites-main.o libsnp-sites.la -lpthread -lz -lm libtool: link: gcc --std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/snp-sites snp_sites-main.o -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lz -lm make[3]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' make[3]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' make[2]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' make[1]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' dh_auto_test make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' Making check in src make[2]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' make run-all-tests make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-snp-sites.o `test -f '../tests/check-snp-sites.c' || echo './'`../tests/check-snp-sites.c gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo './'`../tests/check-vcf.c gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo './'`../tests/helper-methods.c In file included from ../tests/check-snp-sites.c:23: ../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn': ../tests/check-snp-sites.c:40:147: warning: too many arguments for format [-Wformat-extra-args] 40 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:41:153: warning: too many arguments for format [-Wformat-extra-args] 41 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:42:167: warning: too many arguments for format [-Wformat-extra-args] 42 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_n_as_gap_fn': ../tests/check-snp-sites.c:53:125: warning: too many arguments for format [-Wformat-extra-args] 53 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.vcf", "alignment_file_with_n.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:54:131: warning: too many arguments for format [-Wformat-extra-args] 54 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.phylip", "alignment_file_with_n.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:55:145: warning: too many arguments for format [-Wformat-extra-args] 55 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.snp_sites.aln","alignment_file_with_n.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_gzipped_fn': ../tests/check-snp-sites.c:67:150: warning: too many arguments for format [-Wformat-extra-args] 67 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:68:156: warning: too many arguments for format [-Wformat-extra-args] 68 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:69:170: warning: too many arguments for format [-Wformat-extra-args] 69 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_multiple_lines_per_sequence_fn': ../tests/check-snp-sites.c:79:155: warning: too many arguments for format [-Wformat-extra-args] 79 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:80:161: warning: too many arguments for format [-Wformat-extra-args] 80 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:81:174: warning: too many arguments for format [-Wformat-extra-args] 81 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_pure_mode_fn': ../tests/check-snp-sites.c:91:115: warning: too many arguments for format [-Wformat-extra-args] 91 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.vcf", "pure_mode_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:92:121: warning: too many arguments for format [-Wformat-extra-args] 92 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.phylip", "pure_mode_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:93:134: warning: too many arguments for format [-Wformat-extra-args] 93 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.snp_sites.aln","pure_mode_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_monomorphic_sites_fn': ../tests/check-snp-sites.c:103:139: warning: too many arguments for format [-Wformat-extra-args] 103 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.vcf", "pure_mode_monomorphic_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:104:145: warning: too many arguments for format [-Wformat-extra-args] 104 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.phylip", "pure_mode_monomorphic_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:105:158: warning: too many arguments for format [-Wformat-extra-args] 105 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.snp_sites.aln","pure_mode_monomorphic_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_default_fn': ../tests/check-snp-sites.c:116:176: warning: too many arguments for format [-Wformat-extra-args] 116 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_fn': ../tests/check-snp-sites.c:124:176: warning: too many arguments for format [-Wformat-extra-args] 124 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_with_custom_name_fn': ../tests/check-snp-sites.c:133:138: warning: too many arguments for format [-Wformat-extra-args] 133 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name" ) == 1 ,"Only aln with custom name should be outputted"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_phylip_outputted_with_custom_name_fn': ../tests/check-snp-sites.c:141:122: warning: too many arguments for format [-Wformat-extra-args] 141 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name" ) == 1, "Custom name needs extra extension for phylip" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run-all-tests.o `test -f '../tests/run-all-tests.c' || echo './'`../tests/run-all-tests.c ../tests/check-snp-sites.c: In function 'valid_with_all_outputted_with_custom_name_fn': ../tests/check-snp-sites.c:157:123: warning: too many arguments for format [-Wformat-extra-args] 157 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "some_custom_name.vcf" ) == 1, "Custom name needs extra extension for VCF" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:158:129: warning: too many arguments for format [-Wformat-extra-args] 158 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name.phylip" ) == 1, "Custom name needs extra extension for phylip" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:159:143: warning: too many arguments for format [-Wformat-extra-args] 159 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name.snp_sites.aln" ) == 1 , "Custom name needs extra extension for ALN"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_aln_plus_reference_fn': ../tests/check-snp-sites.c:170:182: warning: too many arguments for format [-Wformat-extra-args] 170 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_phylip_plus_reference_fn': ../tests/check-snp-sites.c:178:163: warning: too many arguments for format [-Wformat-extra-args] 178 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "invalid phylib with reference" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o libsnp-sites.la -lpthread -lcheck_pic -lrt -lm -lsubunit -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snp-sites-2.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lcheck_pic -lrt -lsubunit -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make check-TESTS make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' make[4]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' PASS: run-all-tests ============================================================================ Testsuite summary for snp-sites 2.5.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[3]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[2]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[2]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' make[2]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' make[1]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/snp-sites-2.5.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' Making install in src make[2]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1/src' /usr/bin/mkdir -p '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libsnp-sites.so.1.0.0 /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 libtool: install: (cd /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so.1 || { rm -f libsnp-sites.so.1 && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so.1; }; }) libtool: install: (cd /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so || { rm -f libsnp-sites.so && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so; }; }) libtool: install: /usr/bin/install -c .libs/libsnp-sites.lai /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.la libtool: install: /usr/bin/install -c .libs/libsnp-sites.a /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a libtool: install: chmod 644 /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a libtool: install: ranlib /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c snp-sites '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/bin' libtool: warning: 'libsnp-sites.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/snp-sites /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/bin/snp-sites /usr/bin/mkdir -p '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/include/snp-sites' /usr/bin/install -c -m 644 alignment-file.h vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h kseq.h '/build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/include/snp-sites' make[3]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[2]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1/src' make[2]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' make[3]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' 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/snp-sites-2.5.1' make[2]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' make[1]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' dh_install d-shlibmove --commit \ --multiarch \ --exclude-la \ --movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \ debian/tmp/usr/lib/*/libsnp-sites.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.a debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so debian/libsnp-sites1-dev/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/snp-sites-2.5.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libsnp-sites.so.1.0.0 debian/libsnp-sites1/usr/lib/arm-linux-gnueabihf PKGDEV=libsnp-sites1-dev PKGSHL=libsnp-sites1 install -d -m 755 debian/libsnp-sites1-dev/usr/include/snp-sites mv debian/tmp/usr/include/snp-sites/*.h debian/libsnp-sites1-dev/usr/include/snp-sites find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/snp-sites-2.5.1' mkdir -p /build/reproducible-path/snp-sites-2.5.1/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/snp-sites-2.5.1/snp-sites.txt mv /build/reproducible-path/snp-sites-2.5.1/snp-sites.1 /build/reproducible-path/snp-sites-2.5.1/debian/man dh_installman -- make[1]: Leaving directory '/build/reproducible-path/snp-sites-2.5.1' 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libsnp-sites1-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libsnp-sites1-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'snp-sites' in '../snp-sites_2.5.1-2_armhf.deb'. dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.5.1-2_armhf.deb'. dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.5.1-2_armhf.deb'. dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.5.1-2_armhf.deb'. dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.5.1-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../snp-sites_2.5.1-2_armhf.buildinfo dpkg-genchanges --build=binary -O../snp-sites_2.5.1-2_armhf.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/28733 and its subdirectories I: Current time: Tue Dec 17 09:53:15 -12 2024 I: pbuilder-time-stamp: 1734472395 Tue Dec 17 21:53:22 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Tue Dec 17 21:53:22 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Tue Dec 17 21:55:36 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Tue Dec 17 21:55:38 UTC 2024 I: snp-sites_2.5.1-2_armhf.changes: Format: 1.8 Date: Fri, 01 Oct 2021 16:16:44 +0200 Source: snp-sites Binary: libsnp-sites1 libsnp-sites1-dbgsym libsnp-sites1-dev snp-sites snp-sites-dbgsym Architecture: armhf Version: 2.5.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the package snp-sites Changes: snp-sites (2.5.1-2) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * No tab in license text (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit. * Apply multi-arch hints. + libsnp-sites1, libsnp-sites1-dev: Add Multi-Arch: same. * Remove *.la file which should not be installed Checksums-Sha1: 7be7a3c3f9804a6d0afba7a179a18ba0b51c8001 21548 libsnp-sites1-dbgsym_2.5.1-2_armhf.deb 120afa55f32425793097be2fec8c0bd10f8bc5ac 16444 libsnp-sites1-dev_2.5.1-2_armhf.deb 199ba5435f9b55db120118932d3bd094a8dade4c 12752 libsnp-sites1_2.5.1-2_armhf.deb 35ca97286d9725ac6f895090f3cfbbdd95667f43 6372 snp-sites-dbgsym_2.5.1-2_armhf.deb e2a74dee6d5be2d616c94e9ca905e4f446d9202d 7034 snp-sites_2.5.1-2_armhf.buildinfo fdb258d02a7e299c0de0c9ac734479038ef827fc 13376 snp-sites_2.5.1-2_armhf.deb Checksums-Sha256: b1013753d5d8ee3d2ed6f1ed6bebdaddd62180cd594ae0448fb01458d728accd 21548 libsnp-sites1-dbgsym_2.5.1-2_armhf.deb 12d7843cbf111ece4c616e30a2b1efd470b96738143077afef2e5f5dbbcdcafe 16444 libsnp-sites1-dev_2.5.1-2_armhf.deb ed19dfc422dc73b1ed5b22674493a059e0ec06dd677827b832a958ec2f8b3ad0 12752 libsnp-sites1_2.5.1-2_armhf.deb 104d8f767251a899e528f344e1559c5595e56ea867a4e236d4c17e6bb6bff839 6372 snp-sites-dbgsym_2.5.1-2_armhf.deb 6794ca923353fa4e074ff4147d385b4162c1de32f6da84fb53ae795ad8d0cae6 7034 snp-sites_2.5.1-2_armhf.buildinfo f56943933bad813ba4b4d751a24b9550cf945aa65874f7e3f8818a4b2538af10 13376 snp-sites_2.5.1-2_armhf.deb Files: 6ecb43ae6bb318a5c32a0414d814ee4a 21548 debug optional libsnp-sites1-dbgsym_2.5.1-2_armhf.deb 6bb8e7119c46a3e969082f7b7d807029 16444 libdevel optional libsnp-sites1-dev_2.5.1-2_armhf.deb 6dae8e5cac8c04c02154f694e6065b32 12752 libs optional libsnp-sites1_2.5.1-2_armhf.deb cb5f0b5f7614d31c5de449e33545578a 6372 debug optional snp-sites-dbgsym_2.5.1-2_armhf.deb e64296b5f3627c7d6f5ab9039c56d924 7034 science optional snp-sites_2.5.1-2_armhf.buildinfo a57c436eb36ac691e9128a05bb738825 13376 science optional snp-sites_2.5.1-2_armhf.deb Tue Dec 17 21:55:39 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-14002.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OKwz6zqu/snp-sites_2.5.1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OKwz6zqu/snp-sites_2.5.1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OKwz6zqu/snp-sites_2.5.1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OKwz6zqu/b1/snp-sites_2.5.1-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.OKwz6zqu/b2/snp-sites_2.5.1-2_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.336s) 0.336s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 636ms CPU time consumed: 637ms Tue Dec 17 21:55:40 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 17 21:55:40 UTC 2024 I: snp-sites from trixie built successfully and reproducibly on armhf. Tue Dec 17 21:55:41 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 17 21:55:41 UTC 2024 I: Submitting 8.0K b1/snp-sites_2.5.1-2_armhf.buildinfo.asc Tue Dec 17 21:55:42 UTC 2024 I: Submitting 8.0K b2/snp-sites_2.5.1-2_armhf.buildinfo.asc Tue Dec 17 21:55:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 17 21:55:43 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 17 21:55:43 UTC 2024 I: Removing signed snp-sites_2.5.1-2_armhf.buildinfo.asc files: removed './b1/snp-sites_2.5.1-2_armhf.buildinfo.asc' removed './b2/snp-sites_2.5.1-2_armhf.buildinfo.asc'