I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 10 02:04:53 -12 2023 I: pbuilder-time-stamp: 1681135493 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [parsnp_1.7.4+dfsg-2.dsc] I: copying [./parsnp_1.7.4+dfsg.orig.tar.xz] I: copying [./parsnp_1.7.4+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 26 06:18:07 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./parsnp_1.7.4+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting parsnp in parsnp-1.7.4+dfsg dpkg-source: info: unpacking parsnp_1.7.4+dfsg.orig.tar.xz dpkg-source: info: unpacking parsnp_1.7.4+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_missing_interpreter_line.patch dpkg-source: info: applying proper_calls_to_tools.patch dpkg-source: info: applying drop_m64.patch dpkg-source: info: applying fix_build_with_as-needed.patch dpkg-source: info: applying non-versioned-libs.patch dpkg-source: info: applying blhc-fix.patch dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24262/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='24262' 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.Z8yuvHvD/pbuilderrc_AIPb --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Z8yuvHvD/b1 --logfile b1/build.log parsnp_1.7.4+dfsg-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 9 22:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/24262/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, libmuscle-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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 dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{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} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libmagic-mgc{a} libmagic1{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 35.1 MB of archives. After unpacking 149 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1 [26.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1 [9012 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1 [26.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 cython3 arm64 0.29.32-2+b1 [1223 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libmuscle1 arm64 3.7+4565-7 [232 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libmuscle-dev arm64 3.7+4565-7 [293 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1 [9252 B] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1 [1064 B] Get: 57 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1 [1060 B] Get: 58 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1 [26.2 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1 [1068 B] Get: 61 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 35.1 MB in 1s (33.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1_arm64.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1) ... Setting up python3-minimal (3.11.2-1) ... Selecting previously unselected package python3. (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 ... 20364 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1_arm64.deb ... Unpacking python3 (3.11.2-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. 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Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../24-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. 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Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.2-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:arm64 (3.11.2-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-all (3.11.2-1) ... Setting up libpython3-all-dev:arm64 (3.11.2-1) ... Setting up python3-dev (3.11.2-1) ... Setting up python3-all-dev (3.11.2-1) ... Processing triggers for libc-bin (2.36-8) ... 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/parsnp-1.7.4+dfsg/ && 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 > ../parsnp_1.7.4+dfsg-2_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 1.7.4+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf configure.ac:23: warning: AC_OUTPUT should be used without arguments. configure.ac:23: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory, src/Makefile.am:4: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/parsnp-1.7.4+dfsg' dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7 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 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 whether make supports the include directive... yes (GNU style) checking dependency style of gcc... 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 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 libMUSCLE/muscle.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands make[1]: Leaving directory '/build/parsnp-1.7.4+dfsg' dh_auto_build make -j8 make[1]: Entering directory '/build/parsnp-1.7.4+dfsg' Making all in src make[2]: Entering directory '/build/parsnp-1.7.4+dfsg/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector&)': parsnp.cpp:925:24: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=] 925 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~ parsnp.cpp:925:23: note: directive argument in the range [-2147483647, 2147483647] 925 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from parsnp.hh:14, from parsnp.cpp:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'void Aligner::writeOutput(std::string, std::vector&)' at parsnp.cpp:925:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsnp-1.7.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg/src' make[2]: Entering directory '/build/parsnp-1.7.4+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg' make[1]: Leaving directory '/build/parsnp-1.7.4+dfsg' dh_auto_test make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 make[1]: Entering directory '/build/parsnp-1.7.4+dfsg' Making check in src make[2]: Entering directory '/build/parsnp-1.7.4+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg/src' make[2]: Entering directory '/build/parsnp-1.7.4+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg' make[1]: Leaving directory '/build/parsnp-1.7.4+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ make -j8 install DESTDIR=/build/parsnp-1.7.4\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/parsnp-1.7.4+dfsg' Making install in src make[2]: Entering directory '/build/parsnp-1.7.4+dfsg/src' make[3]: Entering directory '/build/parsnp-1.7.4+dfsg/src' /usr/bin/mkdir -p '/build/parsnp-1.7.4+dfsg/debian/parsnp../bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c parsnp_core '/build/parsnp-1.7.4+dfsg/debian/parsnp../bin' make[3]: Leaving directory '/build/parsnp-1.7.4+dfsg/src' make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg/src' make[2]: Entering directory '/build/parsnp-1.7.4+dfsg' make[3]: Entering directory '/build/parsnp-1.7.4+dfsg' 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/parsnp-1.7.4+dfsg' make[2]: Leaving directory '/build/parsnp-1.7.4+dfsg' make[1]: Leaving directory '/build/parsnp-1.7.4+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/parsnp-1.7.4+dfsg' dh_fixperms chmod -x debian/parsnp/usr/share/parsnp/template.ini make[1]: Leaving directory '/build/parsnp-1.7.4+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsnp-dbgsym' in '../parsnp-dbgsym_1.7.4+dfsg-2_arm64.deb'. dpkg-deb: building package 'parsnp' in '../parsnp_1.7.4+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsnp_1.7.4+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../parsnp_1.7.4+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/24262 and its subdirectories I: Current time: Mon Apr 10 02:07:32 -12 2023 I: pbuilder-time-stamp: 1681135652