I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 17 11:10:01 +14 2024 I: pbuilder-time-stamp: 1734383401 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [soapdenovo2_242+dfsg-4.dsc] I: copying [./soapdenovo2_242+dfsg.orig.tar.xz] I: copying [./soapdenovo2_242+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 11 17:12:32 2024 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 ./soapdenovo2_242+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting soapdenovo2 in soapdenovo2-242+dfsg dpkg-source: info: unpacking soapdenovo2_242+dfsg.orig.tar.xz dpkg-source: info: unpacking soapdenovo2_242+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_libsam dpkg-source: info: applying fix_compilation dpkg-source: info: applying fix_usage_name dpkg-source: info: applying add_hardening dpkg-source: info: applying use_debian_zlib dpkg-source: info: applying reproducible dpkg-source: info: applying gcc-10.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3193139/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. 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 Dec 16 21:10 /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/3193139/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3193139/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=561041d8af0a4d3ba313514bb9555a5e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=3193139 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.Q2KqrAAg/pbuilderrc_Z3No --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Q2KqrAAg/b2 --logfile b2/build.log soapdenovo2_242+dfsg-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3193139/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libaio-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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 libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libaio-dev; however: Package libaio-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} intltool-debian{a} libaio-dev{a} libaio1t64{a} libarchive-zip-perl{a} libbam-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 20.9 MB of archives. After unpacking 77.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libaio1t64 amd64 0.3.113-8+b1 [14.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libaio-dev amd64 0.3.113-8+b1 [31.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Fetched 20.9 MB in 0s (63.9 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 ... 19965 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 libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-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 .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libaio1t64:amd64. Preparing to unpack .../29-libaio1t64_0.3.113-8+b1_amd64.deb ... Unpacking libaio1t64:amd64 (0.3.113-8+b1) ... Selecting previously unselected package libaio-dev:amd64. Preparing to unpack .../30-libaio-dev_0.3.113-8+b1_amd64.deb ... Unpacking libaio-dev:amd64 (0.3.113-8+b1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../31-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../32-libbam-dev_0.1.19+dfsg-6_amd64.deb ... Unpacking libbam-dev (0.1.19+dfsg-6) ... Selecting previously unselected package rename. Preparing to unpack .../33-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libaio1t64:amd64 (0.3.113-8+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libaio-dev:amd64 (0.3.113-8+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-4) ... 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: user script /srv/workspace/pbuilder/3193139/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3193139/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/soapdenovo2-242+dfsg/ && 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 > ../soapdenovo2_242+dfsg-4_source.changes dpkg-buildpackage: info: source package soapdenovo2 dpkg-buildpackage: info: source version 242+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' pregraph_sparse_63mer.v1.0.3 cleaning done. SOAPdenovo-63mer cleaning done. SOAPdenovo-fusion cleaning done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_autoreconf_clean -O--no-parallel debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-63mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-127mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' cd sparsePregraph && make clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' pregraph_sparse_63mer.v1.0.3 cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' dh_clean make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel dh_auto_build -O--no-parallel make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' pregraph_sparse_63mer.v1.0.3 cleaning done. Compiling build_graph.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_edge.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling multi_threads.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_preArc.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling pregraph_sparse.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling io_func.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling global.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling convert_soapdenovo.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ pregraph_sparse_63mer.v1.0.3 objects generated. SOAPdenovo-63mer cleaning done. Compiling arc.c... Compiling attachPEinfo.c... Compiling bubble.c... Compiling check.c... Compiling compactEdge.c... Compiling concatenateEdge.c... Compiling connect.c... Compiling contig.c... Compiling cutTipPreGraph.c... Compiling cutTip_graph.c... Compiling darray.c... Compiling dfib.c... Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... Compiling hashFunction.c... Compiling kmer.c... Compiling lib.c... Compiling loadGraph.c... Compiling loadPath.c... Compiling loadPreGraph.c... Compiling localAsm.c... Compiling main.c... Compiling map.c... Compiling mem_manager.c... Compiling newhash.c... Compiling node2edge.c... Compiling orderContig.c... Compiling output_contig.c... Compiling output_pregraph.c... Compiling output_scaffold.c... Compiling pregraph.c... Compiling prlHashCtg.c... Compiling prlHashReads.c... Compiling prlRead2Ctg.c... Compiling prlRead2path.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling readInterval.c... Compiling stack.c... Compiling readseq1by1.c... Compiling scaffold.c... Compiling searchPath.c... Compiling seq.c... Compiling splitReps.c... Compiling cutTip_graph2.c... Compiling linearEdge.c... Compiling kmerhash.c... Compiling read2edge.c... Compiling iterate.c... SOAPdenovo-63mer objects generated. pregraph_sparse_127mer.v1.0.3 cleaning done. Compiling build_graph.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_edge.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling multi_threads.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_preArc.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling pregraph_sparse.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling io_func.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling global.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling convert_soapdenovo.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ pregraph_sparse_127mer.v1.0.3 objects generated. SOAPdenovo-127mer cleaning done. Compiling arc.c... Compiling attachPEinfo.c... Compiling bubble.c... Compiling check.c... Compiling compactEdge.c... Compiling concatenateEdge.c... Compiling connect.c... Compiling contig.c... Compiling cutTipPreGraph.c... Compiling cutTip_graph.c... Compiling darray.c... Compiling dfib.c... Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... Compiling hashFunction.c... Compiling kmer.c... Compiling lib.c... Compiling loadGraph.c... Compiling loadPath.c... Compiling loadPreGraph.c... Compiling localAsm.c... Compiling main.c... Compiling map.c... Compiling mem_manager.c... Compiling newhash.c... Compiling node2edge.c... Compiling orderContig.c... Compiling output_contig.c... Compiling output_pregraph.c... Compiling output_scaffold.c... Compiling pregraph.c... Compiling prlHashCtg.c... Compiling prlHashReads.c... Compiling prlRead2Ctg.c... Compiling prlRead2path.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling readInterval.c... Compiling stack.c... Compiling readseq1by1.c... Compiling scaffold.c... Compiling searchPath.c... Compiling seq.c... Compiling splitReps.c... Compiling cutTip_graph2.c... Compiling linearEdge.c... Compiling kmerhash.c... Compiling read2edge.c... Compiling iterate.c... SOAPdenovo-127mer objects generated. Compiling searchPath.c... Compiling scaffold.c... Compiling check.c... Compiling seq.c... Compiling bundle.c... Compiling potential.c... Compiling loadGraph.c... Compiling mem_manager.c... Compiling attachPEinfo.c... Compiling newhash.c... Compiling output_scaffold.c... Compiling orderContig.c... Compiling connect.c... Compiling hashFunction.c... Compiling readseq1by1.c... Compiling fib.c... Compiling fibHeap.c... Compiling stack.c... Compiling kmer.c... Compiling prepare.c... Compiling prlHashCtg.c... Compiling prlRead2Ctg.c... Compiling map.c... Compiling localAsm.c... Compiling lib.c... Compiling darray.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling main.c... Making SOAPdenovo-fusion... SOAPdenovo-fusion compilation done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_auto_test -O--no-parallel create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install --destdir=debian/soapdenovo2/ -O--no-parallel debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_install cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP* make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'soapdenovo2' in '../soapdenovo2_242+dfsg-4_amd64.deb'. dpkg-deb: building package 'soapdenovo2-dbgsym' in '../soapdenovo2-dbgsym_242+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../soapdenovo2_242+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../soapdenovo2_242+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3193139/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3193139/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/3193139 and its subdirectories I: Current time: Tue Dec 17 11:13:58 +14 2024 I: pbuilder-time-stamp: 1734383638