I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 17 11:22:26 -12 2024 I: pbuilder-time-stamp: 1721258546 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/16779/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='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='b8cca543e7694d898634a3e38f5f52b3' 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='16779' 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.2OIwwUDj/pbuilderrc_X47B --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2OIwwUDj/b1 --logfile b1/build.log snp-sites_2.5.1-2.dsc' SUDO_GID='113' SUDO_UID='107' 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 ff4a 6.1.0-23-armmp-lpae #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/16779/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 ... 19503 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 28.2 MB of archives. After unpacking 102 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf openssl armhf 3.2.2-1 [1329 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-1 [195 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-1 [87.8 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.1-2 [1376 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf rubygems-integration all 1.18 [6704 B] Get: 14 http://deb.debian.org/debian unstable/main armhf rake all 13.2.1-1 [65.2 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf ruby-sdbm armhf 1.0.0-5+b4 [13.3 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libedit2 armhf 3.1-20240517-1 [77.7 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2 [81.8 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libyaml-0-2 armhf 0.2.5-1+b1 [45.5 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libruby3.1t64 armhf 3.1.2-8.3 [5068 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf ruby3.1 armhf 3.1.2-8.3 [663 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 25 http://deb.debian.org/debian unstable/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 27 http://deb.debian.org/debian unstable/main armhf ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf asciidoctor all 2.0.20-1 [87.7 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-1 [723 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libsubunit0 armhf 1.4.2-3 [5920 B] Get: 35 http://deb.debian.org/debian unstable/main armhf libsubunit-dev armhf 1.4.2-3 [7060 B] Get: 36 http://deb.debian.org/debian unstable/main armhf check armhf 0.15.2-2+b1 [109 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf d-shlibs all 0.106 [10.9 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.16 [88.6 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg-3+b1 [583 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-1 [1479 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf debhelper all 13.16 [891 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-3 [31.7 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-3 [29.1 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-3 [26.1 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf pkg-config armhf 1.8.1-3 [13.9 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Fetched 28.2 MB in 2s (16.0 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 ... 19503 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_3.2.2-1_armhf.deb ... Unpacking openssl (3.2.2-1) ... 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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-1_armhf.deb ... Unpacking gettext-base (0.22.5-1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-1_armhf.deb ... Unpacking bsdextrautils (2.40.2-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.1-2_armhf.deb ... Unpacking man-db (2.12.1-2) ... 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 ruby-sdbm:armhf. Preparing to unpack .../17-ruby-sdbm_1.0.0-5+b4_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b4) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../18-libedit2_3.1-20240517-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20240517-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../19-libncurses6_6.5-2_armhf.deb ... Unpacking libncurses6:armhf (6.5-2) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../20-libyaml-0-2_0.2.5-1+b1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:armhf. Preparing to unpack .../21-libruby3.1t64_3.1.2-8.3_armhf.deb ... Unpacking libruby3.1t64:armhf (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../22-ruby3.1_3.1.2-8.3_armhf.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../23-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... 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_2.0.20-1_all.deb ... Unpacking ruby-asciidoctor (2.0.20-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../27-asciidoctor_2.0.20-1_all.deb ... Unpacking asciidoctor (2.0.20-1) ... 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_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.22.5-1_all.deb ... Unpacking autopoint (0.22.5-1) ... Selecting previously unselected package libsubunit0:armhf. Preparing to unpack .../33-libsubunit0_1.4.2-3_armhf.deb ... Unpacking libsubunit0:armhf (1.4.2-3) ... Selecting previously unselected package libsubunit-dev:armhf. Preparing to unpack .../34-libsubunit-dev_1.4.2-3_armhf.deb ... Unpacking libsubunit-dev:armhf (1.4.2-3) ... 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_0.106_all.deb ... Unpacking d-shlibs (0.106) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../37-libdebhelper-perl_13.16_all.deb ... Unpacking libdebhelper-perl (13.16) ... Selecting previously unselected package libtool. Preparing to unpack .../38-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_0.191-2_armhf.deb ... Unpacking libelf1t64:armhf (0.191-2) ... 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_armhf.deb ... Unpacking libicu72:armhf (72.1-5) ... Selecting previously unselected package libxml2:armhf. 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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 vcf.c -fPIC -DPIC -o .libs/vcf.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 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 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:980, 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 snp-sites.c -fPIC -DPIC -o .libs/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 alignment-file.c -o alignment-file.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 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': 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: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" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.5.1-2_armhf.deb'. dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-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/16779 and its subdirectories I: Current time: Wed Jul 17 11:24:19 -12 2024 I: pbuilder-time-stamp: 1721258659