I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 7 18:48:14 +14 2024 I: pbuilder-time-stamp: 1712465294 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 [vcftools_0.1.16-3.dsc] I: copying [./vcftools_0.1.16.orig.tar.gz] I: copying [./vcftools_0.1.16-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 7 06:07:18 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found dpkg-source: info: extracting vcftools in vcftools-0.1.16 dpkg-source: info: unpacking vcftools_0.1.16.orig.tar.gz dpkg-source: info: unpacking vcftools_0.1.16-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying temporary_test_fix.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpage.patch dpkg-source: info: applying 0001-vcf-fix-ploidy-make-p-work-without-.-on-INC.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10279/tmp/hooks/D01_modify_environment starting debug: Running on ff64a. 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 Apr 7 04:49 /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/10279/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/10279/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=aa7a4bd6480f402082be5c0db3191b2e LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=10279 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.asdQzK23/pbuilderrc_c1V3 --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.asdQzK23/b2 --logfile b2/build.log vcftools_0.1.16-3.dsc' SUDO_GID=114 SUDO_UID=109 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 6 11:27 /bin -> usr/bin I: user script /srv/workspace/pbuilder/10279/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, zlib1g-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 ... 19637 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{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, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 70.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Fetched 19.3 MB in 2s (10.7 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 ... 19637 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%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.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. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../22-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../30-libpkgconf3_1.8.1-1+b2_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../31-pkgconf-bin_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../32-pkgconf_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:armhf. Preparing to unpack .../33-pkg-config_1.8.1-1+b2_armhf.deb ... Unpacking pkg-config:armhf (1.8.1-1+b2) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-15) ... 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/10279/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/10279/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/vcftools-0.1.16/ && 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 > ../vcftools_0.1.16-3_source.changes dpkg-buildpackage: info: source package vcftools dpkg-buildpackage: info: source version 0.1.16-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/vcftools.substvars debian/files rm -fr -- debian/vcftools/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_configure -- --with-pmdir=/share/perl5 ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-pmdir=/share/perl5 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 g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes 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 arpa/inet.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for netdb.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for int8_t... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for error_at_line... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... yes checking for memset... yes checking for pow... no checking for select... yes checking for socket... yes checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for strtol... 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: creating src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_build make -j6 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make all-recursive make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making all in src make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making all in cpp make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp bgzf.c: In function 'bgzf_check_EOF': bgzf.c:60:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgzf.c:622:9: note: in expansion of macro '_bgzf_read' 622 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp In file included from /usr/include/c++/13/vector:72, from entry.h:12, from bcf_entry.h:10, from bcf_entry_setters.cpp:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bcf_entry::set_indv_GQUALITY(unsigned int, const float&)' at bcf_entry_setters.cpp:333:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bcf_entry::set_indv_GQUALITY(unsigned int, const std::vector&)' at bcf_entry_setters.cpp:316:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp gcc -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp variant_file_filters.cpp: In member function 'void variant_file::filter_individuals_randomly(int)': variant_file_filters.cpp:129:23: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from variant_file.h:15, from variant_file_filters.cpp:7: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/algorithm:60, from variant_file.h:15, from variant_file_output.cpp:8: /usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': variant_file_output.cpp:4426:39: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp In file included from /usr/include/c++/13/vector:72, from entry.h:12, from vcf_entry.h:12, from vcf_entry_setters.cpp:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void vcf_entry::set_indv_GQUALITY(unsigned int, double)' at vcf_entry_setters.cpp:181:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/set:62, from variant_file.h:26: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from variant_file.h:24: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63, from variant_file.h:28: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'void variant_file::output_TsTv_by_quality(const parameters&)' at variant_file_output.cpp:3277:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'void variant_file::output_TsTv_by_quality(const parameters&)' at variant_file_output.cpp:3279:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void variant_file::output_Tajima_D(const parameters&)' at variant_file_output.cpp:4015:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/vcftools-0.1.16=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making all in perl make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_auto_test make -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making check in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making check in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making check in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -fr -- /tmp/dh-xdg-rundir-xCfXhRnt create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/vcftools.substvars rm -fr -- debian/.debhelper/generated/vcftools/ debian/vcftools/ debian/tmp/ dh_auto_install --destdir=debian/vcftools/ install -m0755 -d /build/reproducible-path/vcftools-0.1.16/debian/vcftools make -j6 install DESTDIR=/build/reproducible-path/vcftools-0.1.16/debian/vcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' Making install in src make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' Making install in cpp make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' /usr/bin/install -c vcftools '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 vcftools.1 '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/man/man1' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/cpp' Making install in perl make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src/perl' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' /usr/bin/mkdir -p '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr//share/perl5' /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/bin' make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src/perl' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Entering directory '/build/reproducible-path/vcftools-0.1.16/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16/src' make[2]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Entering directory '/build/reproducible-path/vcftools-0.1.16' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[2]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_install for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installdocs install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -m0755 -d debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/README.test debian/vcftools/usr/share/doc/vcftools cp --reflink=auto -a ./debian/tests/run-unit-test debian/vcftools/usr/share/doc/vcftools chmod -R u\+rw,go=rX debian/vcftools/usr/share/doc install -p -m0644 debian/copyright debian/vcftools/usr/share/doc/vcftools/copyright rm -f debian/vcftools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installchangelogs src/perl/ChangeLog install -m0755 -d debian/vcftools/usr/share/doc/vcftools install -p -m0644 debian/.debhelper/generated/vcftools/dh_installchangelogs.dch.trimmed debian/vcftools/usr/share/doc/vcftools/changelog.Debian install -p -m0644 src/perl/ChangeLog debian/vcftools/usr/share/doc/vcftools/changelog make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' rm -f debian/vcftools.debhelper.log debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/vcftools-0.1.16' dh_installexamples; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite; mkdir -p /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata; cp ./examples/* /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata/; find ./src/perl/ \( -name "*.pm" -o -name "*fill*" -o -name "test.t" \) -exec cp \{\} /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \; sed -i 's#examples#testdata#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#I\.\./perl/#I\.\./\.#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; sed -i 's#\.\./perl/#/usr/bin/#g' /build/reproducible-path/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t; for perlscript in `grep -lR '#!/usr/bin/env \+perl' debian/*/usr/share/doc/vcftools/examples` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/vcftools-0.1.16' dh_installman install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-aa.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-fs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/fill-rsIDs.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-annotate.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-isec.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-merge.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-query.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-sort.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-stats.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./debian/mans/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 install -m0755 -d debian/vcftools/usr/share/man/man1/ install -p -m0644 ./src/cpp/vcftools.1 debian/vcftools/usr/share/man/man1/vcftools.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/vcftools.1.dh-new debian/vcftools/usr/share/man/man1/vcftools.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcftools.1 mv debian/vcftools/usr/share/man/man1/fill-aa.1.dh-new debian/vcftools/usr/share/man/man1/fill-aa.1 mv debian/vcftools/usr/share/man/man1/fill-an-ac.1.dh-new debian/vcftools/usr/share/man/man1/fill-an-ac.1 mv debian/vcftools/usr/share/man/man1/fill-fs.1.dh-new debian/vcftools/usr/share/man/man1/fill-fs.1 mv debian/vcftools/usr/share/man/man1/fill-ref-md5.1.dh-new debian/vcftools/usr/share/man/man1/fill-ref-md5.1 mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-aa.1 debian/vcftools/usr/share/man/man1/fill-an-ac.1 debian/vcftools/usr/share/man/man1/fill-fs.1 debian/vcftools/usr/share/man/man1/fill-ref-md5.1 debian/vcftools/usr/share/man/man1/fill-rsIDs.1 mv debian/vcftools/usr/share/man/man1/vcf-annotate.1.dh-new debian/vcftools/usr/share/man/man1/vcf-annotate.1 mv debian/vcftools/usr/share/man/man1/vcf-compare.1.dh-new debian/vcftools/usr/share/man/man1/vcf-compare.1 mv debian/vcftools/usr/share/man/man1/vcf-concat.1.dh-new debian/vcftools/usr/share/man/man1/vcf-concat.1 mv debian/vcftools/usr/share/man/man1/vcf-consensus.1.dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 mv debian/vcftools/usr/share/man/man1/vcf-contrast.1.dh-new debian/vcftools/usr/share/man/man1/vcf-contrast.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-annotate.1 debian/vcftools/usr/share/man/man1/vcf-compare.1 debian/vcftools/usr/share/man/man1/vcf-concat.1 debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 mv debian/vcftools/usr/share/man/man1/vcf-convert.1.dh-new debian/vcftools/usr/share/man/man1/vcf-convert.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 mv debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1.dh-new debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 mv debian/vcftools/usr/share/man/man1/vcf-indel-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-isec.1.dh-new debian/vcftools/usr/share/man/man1/vcf-isec.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1 debian/vcftools/usr/share/man/man1/vcf-fix-ploidy.1 debian/vcftools/usr/share/man/man1/vcf-indel-stats.1 debian/vcftools/usr/share/man/man1/vcf-isec.1 mv debian/vcftools/usr/share/man/man1/vcf-stats.1.dh-new debian/vcftools/usr/share/man/man1/vcf-stats.1 mv debian/vcftools/usr/share/man/man1/vcf-subset.1.dh-new debian/vcftools/usr/share/man/man1/vcf-subset.1 mv debian/vcftools/usr/share/man/man1/vcf-to-tab.1.dh-new debian/vcftools/usr/share/man/man1/vcf-to-tab.1 mv debian/vcftools/usr/share/man/man1/vcf-tstv.1.dh-new debian/vcftools/usr/share/man/man1/vcf-tstv.1 mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-stats.1 debian/vcftools/usr/share/man/man1/vcf-subset.1 debian/vcftools/usr/share/man/man1/vcf-to-tab.1 debian/vcftools/usr/share/man/man1/vcf-tstv.1 debian/vcftools/usr/share/man/man1/vcf-validator.1 mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1 mv debian/vcftools/usr/share/man/man1/vcf-phased-join.1.dh-new debian/vcftools/usr/share/man/man1/vcf-phased-join.1 mv debian/vcftools/usr/share/man/man1/vcf-query.1.dh-new debian/vcftools/usr/share/man/man1/vcf-query.1 mv debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1.dh-new debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 mv debian/vcftools/usr/share/man/man1/vcf-sort.1.dh-new debian/vcftools/usr/share/man/man1/vcf-sort.1 chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-merge.1 debian/vcftools/usr/share/man/man1/vcf-phased-join.1 debian/vcftools/usr/share/man/man1/vcf-query.1 debian/vcftools/usr/share/man/man1/vcf-shuffle-cols.1 debian/vcftools/usr/share/man/man1/vcf-sort.1 dh_perl mv debian/vcftools.substvars.new debian/vcftools.substvars rmdir --ignore-fail-on-non-empty --parents debian/vcftools/usr/share/perl5 dh_link dh_strip_nondeterminism dh_compress cd debian/vcftools chmod a-x usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 gzip -9nf usr/share/doc/vcftools/changelog usr/share/doc/vcftools/changelog.Debian usr/share/man/man1/fill-aa.1 usr/share/man/man1/fill-an-ac.1 usr/share/man/man1/fill-fs.1 usr/share/man/man1/fill-ref-md5.1 usr/share/man/man1/fill-rsIDs.1 usr/share/man/man1/vcf-annotate.1 usr/share/man/man1/vcf-compare.1 usr/share/man/man1/vcf-concat.1 usr/share/man/man1/vcf-consensus.1 usr/share/man/man1/vcf-contrast.1 usr/share/man/man1/vcf-convert.1 usr/share/man/man1/vcf-fix-newlines.1 usr/share/man/man1/vcf-fix-ploidy.1 usr/share/man/man1/vcf-indel-stats.1 usr/share/man/man1/vcf-isec.1 usr/share/man/man1/vcf-merge.1 usr/share/man/man1/vcf-phased-join.1 usr/share/man/man1/vcf-query.1 usr/share/man/man1/vcf-shuffle-cols.1 usr/share/man/man1/vcf-sort.1 usr/share/man/man1/vcf-stats.1 usr/share/man/man1/vcf-subset.1 usr/share/man/man1/vcf-to-tab.1 usr/share/man/man1/vcf-tstv.1 usr/share/man/man1/vcf-validator.1 usr/share/man/man1/vcftools.1 cd '/build/reproducible-path/vcftools-0.1.16' dh_fixperms find debian/vcftools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/vcftools/usr/share/doc -type f -a -true -a ! -regex 'debian/vcftools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/vcftools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/share/perl5 -type f -perm -5 -name '*.pm' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a-X find debian/vcftools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/vcftools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/vcftools/usr/bin/vcftools dh_strip -a install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/cd objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/cd/44537dfc8277e3ebb9c9e150fc9ccb3f55e061.debug chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/cd/44537dfc8277e3ebb9c9e150fc9ccb3f55e061.debug strip --remove-section=.comment --remove-section=.note debian/vcftools/usr/bin/vcftools objcopy --add-gnu-debuglink debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/cd/44537dfc8277e3ebb9c9e150fc9ccb3f55e061.debug debian/vcftools/usr/bin/vcftools install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/usr/share/doc ln -s vcftools debian/.debhelper/vcftools/dbgsym-root/usr/share/doc/vcftools-dbgsym install -m0755 -d debian/.debhelper/vcftools dh_makeshlibs -a rm -f debian/vcftools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/vcftools/DEBIAN dpkg-shlibdeps -Tdebian/vcftools.substvars debian/vcftools/usr/bin/vcftools dpkg-shlibdeps: warning: debian/vcftools/usr/bin/vcftools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb install -m0755 -d debian/vcftools/DEBIAN dh_gencontrol install -m0755 -d debian/vcftools/DEBIAN echo misc:Depends= >> debian/vcftools.substvars echo misc:Pre-Depends= >> debian/vcftools.substvars install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=cd44537dfc8277e3ebb9c9e150fc9ccb3f55e061 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -cdebian/control -Pdebian/vcftools chmod 0644 -- debian/vcftools/DEBIAN/control dh_md5sums install -m0755 -d debian/vcftools/DEBIAN cd debian/vcftools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/vcftools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/vcftools/dbgsym-root/DEBIAN cd debian/.debhelper/vcftools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/vcftools .. dpkg-deb --root-owner-group --build debian/.debhelper/vcftools/dbgsym-root .. dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-3_armhf.deb'. dpkg-deb: building package 'vcftools-dbgsym' in '../vcftools-dbgsym_0.1.16-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../vcftools_0.1.16-3_armhf.buildinfo dpkg-genchanges --build=binary -O../vcftools_0.1.16-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/10279/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/10279/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/10279 and its subdirectories I: Current time: Sun Apr 7 19:11:30 +14 2024 I: pbuilder-time-stamp: 1712466690