I: pbuilder: network access will be disabled during build I: Current time: Mon May 6 23:56:01 +14 2024 I: pbuilder-time-stamp: 1714989361 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 [skesa_2.4.0-6.dsc] I: copying [./skesa_2.4.0.orig.tar.gz] I: copying [./skesa_2.4.0-6.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 22 18:35:32 2023 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./skesa_2.4.0-6.dsc: no acceptable signature found dpkg-source: info: extracting skesa in skesa-2.4.0 dpkg-source: info: unpacking skesa_2.4.0.orig.tar.gz dpkg-source: info: unpacking skesa_2.4.0-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_ngs-sdk.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying link_boost_dynamically.patch dpkg-source: info: applying no_sse4.2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 6 09:56 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8cbf7f21fd5a4f1f855531f55736f8b4 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1800144 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pbGK8fmS/pbuilderrc_d4vt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pbGK8fmS/b2 --logfile b2/build.log skesa_2.4.0-6.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1800144/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), libboost-dev, libboost-chrono-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-regex-dev, libboost-system-dev, libboost-timer-dev, libncbi-vdb-dev (>= 3), libngs-c++-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 ... 19744 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 libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-chrono-dev; however: Package libboost-chrono-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however: Package libboost-timer-dev is not installed. pbuilder-satisfydepends-dummy depends on libncbi-vdb-dev (>= 3); however: Package libncbi-vdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libngs-c++-dev; however: Package libngs-c++-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost1.83-dev{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libncbi-vdb-dev{a} libncbi-vdb3{a} libncbi-wvdb-dev{a} libncbi-wvdb3{a} libngs-c++-dev{a} libngs-c++3{a} libpipeline1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} ncbi-vdb-data{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 49.6 MB of archives. After unpacking 342 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-4+b1 [194 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1 [7664 B] Get: 34 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1 [19.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-2.1+b1 [10.6 MB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-2.1+b1 [239 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83-dev arm64 1.83.0-2.1+b1 [244 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libboost-chrono-dev arm64 1.83.0.2+b2 [4212 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 40 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-2.1+b1 [311 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-4+b1 [10.2 MB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-2.1+b1 [334 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-2.1+b1 [261 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2.1+b1 [331 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libboost-program-options1.83-dev arm64 1.83.0-2.1+b1 [369 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 48 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-2.1+b1 [230 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-2.1+b1 [231 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 52 http://deb.debian.org/debian unstable/main arm64 libboost-timer1.83.0 arm64 1.83.0-2.1+b1 [234 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libboost-timer1.83-dev arm64 1.83.0-2.1+b1 [236 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libboost-timer-dev arm64 1.83.0.2+b2 [3712 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2+b1 [985 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libncbi-wvdb3 arm64 3.0.2+dfsg-2+b1 [1010 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libncbi-wvdb-dev arm64 3.0.2+dfsg-2+b1 [1161 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.5+dfsg2-2 [323 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb-dev arm64 3.0.2+dfsg-2+b1 [1438 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libngs-c++3 arm64 3.0.3+dfsg-7 [121 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libngs-c++-dev arm64 3.0.3+dfsg-7 [187 kB] Fetched 49.6 MB in 0s (162 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 ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-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 .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/skesa-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../skesa_2.4.0-6_source.changes dpkg-buildpackage: info: source package skesa dpkg-buildpackage: info: source version 2.4.0-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Aaron M. Ucko dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/skesa-2.4.0' rm -f skesa gfa_connector kmercounter *.o /build/reproducible-path/skesa-2.4.0/NGS/ngs.done make[1]: Leaving directory '/build/reproducible-path/skesa-2.4.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/skesa-2.4.0' c++ -std=c++11 -fdiagnostics-color=never -c -o skesa.o skesa.cpp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/skesa-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -I /build/reproducible-path/skesa-2.4.0/NGS/ngs_out/include -I /build/reproducible-path/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o glb_align.o glb_align.cpp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/skesa-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -I /build/reproducible-path/skesa-2.4.0/NGS/ngs_out/include -I /build/reproducible-path/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o gfa_connector.o gfa_connector.cpp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/skesa-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -I /build/reproducible-path/skesa-2.4.0/NGS/ngs_out/include -I /build/reproducible-path/skesa-2.4.0/NGS/vdb_out/include c++ -std=c++11 -fdiagnostics-color=never -c -o kmercounter.o kmercounter.cpp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/skesa-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing -fomit-frame-pointer -I /build/reproducible-path/skesa-2.4.0/NGS/ngs_out/include -I /build/reproducible-path/skesa-2.4.0/NGS/vdb_out/include cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ glb_align.cpp: In function 'DeBruijn::CCigar DeBruijn::GlbAlign(const char*, int, const char*, int, int, int, const char (*)[256])': glb_align.cpp:399:13: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 399 | mtrx[0] = 0; | ~~~~~~~~^~~ In constructor 'DeBruijn::SRawMemory::SRawMemory(size_t, size_t)', inlined from 'DeBruijn::CCigar DeBruijn::GlbAlign(const char*, int, const char*, int, int, int, const char (*)[256])' at glb_align.cpp:380:29: glb_align.cpp:355:39: note: destination object of size 0 allocated by 'operator new []' 355 | mtrx = new char[(na+1)*(nb+1)]; | ^ glb_align.cpp: In function 'DeBruijn::CCigar DeBruijn::LclAlign(const char*, int, const char*, int, int, int, bool, bool, const char (*)[256])': glb_align.cpp:556:13: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 556 | mtrx[0] = 0; | ~~~~~~~~^~~ In constructor 'DeBruijn::SRawMemory::SRawMemory(size_t, size_t)', inlined from 'DeBruijn::CCigar DeBruijn::LclAlign(const char*, int, const char*, int, int, int, bool, bool, const char (*)[256])' at glb_align.cpp:545:29: glb_align.cpp:355:39: note: destination object of size 0 allocated by 'operator new []' 355 | mtrx = new char[(na+1)*(nb+1)]; | ^ In file included from /usr/include/c++/13/string:51, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from skesa.cpp:27: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = char; _Up = char; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*; _Tp = char]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = char; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:781:34: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: argument 1 null where non-null expected [-Wnonnull] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:437:30: note: in a call to built-in function 'void* __builtin_memmove(void*, const void*, long unsigned int)' In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const char; _Up = char; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const char*; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = char*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = char*; _Tp = char]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = char; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:781:34: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: argument 1 null where non-null expected [-Wnonnull] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:437:30: note: in a call to built-in function 'void* __builtin_memmove(void*, const void*, long unsigned int)' c++ -std=c++11 -fdiagnostics-color=never -o kmercounter kmercounter.o glb_align.o -lngs-c++ -lncbi-vdb -lzstd -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -lrt -ldl -lm -lpthread -lz c++ -std=c++11 -fdiagnostics-color=never -o gfa_connector gfa_connector.o glb_align.o -lngs-c++ -lncbi-vdb -lzstd -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -lrt -ldl -lm -lpthread -lz c++ -std=c++11 -fdiagnostics-color=never -o skesa skesa.o glb_align.o -lngs-c++ -lncbi-vdb -lzstd -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -lrt -ldl -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/skesa-2.4.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/skesa/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/skesa/usr/bin/skesa was not linked against libncbi-vdb.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'skesa' in '../skesa_2.4.0-6_arm64.deb'. dpkg-deb: building package 'skesa-dbgsym' in '../skesa-dbgsym_2.4.0-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../skesa_2.4.0-6_arm64.buildinfo dpkg-genchanges --build=binary -O../skesa_2.4.0-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1800144/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1800144 and its subdirectories I: Current time: Tue May 7 00:00:02 +14 2024 I: pbuilder-time-stamp: 1714989602