I: pbuilder: network access will be disabled during build
I: Current time: Fri May 31 12:11:09 +14 2024
I: pbuilder-time-stamp: 1717107069
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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 20:07:18 2021 +14
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/14261/tmp/hooks/D01_modify_environment starting
debug: Running on codethink13-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 31 12:11 /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/14261/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/14261/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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=arm64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/var/lib/jenkins
HOSTNAME=i-capture-the-hostname
HOSTTYPE=aarch64
HOST_ARCH=arm64
IFS='
'
LANG=C
LANGUAGE=nl_BE:nl
LC_ALL=C
MACHTYPE=aarch64-unknown-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=14261
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.vQyBtyOT/pbuilderrc_8Bo1 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vQyBtyOT/b2 --logfile b2/build.log --extrapackages usrmerge vcftools_0.1.16-3.dsc'
SUDO_GID=117
SUDO_UID=110
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
USERNAME=root
_='I: set'
http_proxy=http://192.168.101.16:3128
I: uname -a
Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 May 29 06:48 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/14261/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19616 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on 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 19.4 MB of archives. After unpacking 76.0 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB]
Fetched 19.4 MB in 1s (35.8 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 ... 19616 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
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_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
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_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
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:arm64.
Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ...
Unpacking libelf1:arm64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_arm64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ...
Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_arm64.deb ...
Unpacking gettext (0.21-12) ...
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_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package libpkgconf3:arm64.
Preparing to unpack .../30-libpkgconf3_1.8.1-1_arm64.deb ...
Unpacking libpkgconf3:arm64 (1.8.1-1) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../31-pkgconf-bin_1.8.1-1_arm64.deb ...
Unpacking pkgconf-bin (1.8.1-1) ...
Selecting previously unselected package pkgconf:arm64.
Preparing to unpack .../32-pkgconf_1.8.1-1_arm64.deb ...
Unpacking pkgconf:arm64 (1.8.1-1) ...
Selecting previously unselected package pkg-config:arm64.
Preparing to unpack .../33-pkg-config_1.8.1-1_arm64.deb ...
Unpacking pkg-config:arm64 (1.8.1-1) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../34-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ...
Setting up libpipeline1:arm64 (1.5.7-1) ...
Setting up libicu72:arm64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:arm64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:arm64 (1.8.1-1) ...
Setting up autopoint (0.21-12) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up pkgconf:arm64 (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up pkg-config:arm64 (1.8.1-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-9) ...
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
Reading package lists...
Building dependency tree...
Reading state information...
usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/14261/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
I: user script /srv/workspace/pbuilder/14261/tmp/hooks/A99_set_merged_usr finished
hostname: Temporary failure in name resolution
I: Running cd /build/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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
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/vcftools-0.1.16'
dh_auto_configure -- --with-pmdir=/share/perl5
./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-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... no
checking for error_at_line... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
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/vcftools-0.1.16'
dh_auto_build
make -j8
make[1]: Entering directory '/build/vcftools-0.1.16'
make all-recursive
make[2]: Entering directory '/build/vcftools-0.1.16'
Making all in src
make[3]: Entering directory '/build/vcftools-0.1.16/src'
Making all in cpp
make[4]: Entering directory '/build/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -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
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp
In file included from /usr/include/c++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/algorithm:60,
from variant_file.h:15,
from variant_file_output.cpp:8:
/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper<typename decay<_Tp2>::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper<typename decay<_Tp>::type>::__type = double; typename decay<_Tp>::type = double]':
variant_file_output.cpp:4426:39: required from here
/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
741 | make_pair(_T1&& __x, _T2&& __y)
| ^~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/vcftools-0.1.16=. -fstack-protector-strong -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/vcftools-0.1.16/src/cpp'
Making all in perl
make[4]: Entering directory '/build/vcftools-0.1.16/src/perl'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/build/vcftools-0.1.16/src/perl'
make[4]: Entering directory '/build/vcftools-0.1.16/src'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/vcftools-0.1.16/src'
make[3]: Leaving directory '/build/vcftools-0.1.16/src'
make[3]: Entering directory '/build/vcftools-0.1.16'
make[3]: Leaving directory '/build/vcftools-0.1.16'
make[2]: Leaving directory '/build/vcftools-0.1.16'
make[1]: Leaving directory '/build/vcftools-0.1.16'
dh_auto_test
make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
make[1]: Entering directory '/build/vcftools-0.1.16'
Making check in src
make[2]: Entering directory '/build/vcftools-0.1.16/src'
Making check in cpp
make[3]: Entering directory '/build/vcftools-0.1.16/src/cpp'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/vcftools-0.1.16/src/cpp'
Making check in perl
make[3]: Entering directory '/build/vcftools-0.1.16/src/perl'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/vcftools-0.1.16/src/perl'
make[3]: Entering directory '/build/vcftools-0.1.16/src'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/vcftools-0.1.16/src'
make[2]: Leaving directory '/build/vcftools-0.1.16/src'
make[2]: Entering directory '/build/vcftools-0.1.16'
make[2]: Leaving directory '/build/vcftools-0.1.16'
make[1]: Leaving directory '/build/vcftools-0.1.16'
rm -fr -- /tmp/dh-xdg-rundir-pfaMDiNF
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/vcftools-0.1.16/debian/vcftools
make -j8 install DESTDIR=/build/vcftools-0.1.16/debian/vcftools AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/vcftools-0.1.16'
Making install in src
make[2]: Entering directory '/build/vcftools-0.1.16/src'
Making install in cpp
make[3]: Entering directory '/build/vcftools-0.1.16/src/cpp'
make[4]: Entering directory '/build/vcftools-0.1.16/src/cpp'
/usr/bin/mkdir -p '/build/vcftools-0.1.16/debian/vcftools/usr/bin'
/usr/bin/mkdir -p '/build/vcftools-0.1.16/debian/vcftools/usr/share/man/man1'
/usr/bin/install -c vcftools '/build/vcftools-0.1.16/debian/vcftools/usr/bin'
/usr/bin/install -c -m 644 vcftools.1 '/build/vcftools-0.1.16/debian/vcftools/usr/share/man/man1'
make[4]: Leaving directory '/build/vcftools-0.1.16/src/cpp'
make[3]: Leaving directory '/build/vcftools-0.1.16/src/cpp'
Making install in perl
make[3]: Entering directory '/build/vcftools-0.1.16/src/perl'
make[4]: Entering directory '/build/vcftools-0.1.16/src/perl'
/usr/bin/mkdir -p '/build/vcftools-0.1.16/debian/vcftools/usr/bin'
/usr/bin/mkdir -p '/build/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/vcftools-0.1.16/debian/vcftools/usr/bin'
/usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/build/vcftools-0.1.16/debian/vcftools/usr//share/perl5'
make[4]: Leaving directory '/build/vcftools-0.1.16/src/perl'
make[3]: Leaving directory '/build/vcftools-0.1.16/src/perl'
make[3]: Entering directory '/build/vcftools-0.1.16/src'
make[4]: Entering directory '/build/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/vcftools-0.1.16/src'
make[3]: Leaving directory '/build/vcftools-0.1.16/src'
make[2]: Leaving directory '/build/vcftools-0.1.16/src'
make[2]: Entering directory '/build/vcftools-0.1.16'
make[3]: Entering directory '/build/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/vcftools-0.1.16'
make[2]: Leaving directory '/build/vcftools-0.1.16'
make[1]: Leaving directory '/build/vcftools-0.1.16'
rm -f debian/vcftools.debhelper.log
debian/rules override_dh_install
make[1]: Entering directory '/build/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/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/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/vcftools-0.1.16'
rm -f debian/vcftools.debhelper.log
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/vcftools-0.1.16'
dh_installexamples;
mkdir -p /build/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite;
mkdir -p /build/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testdata;
cp ./examples/* /build/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/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite \;
sed -i 's#examples#testdata#g' /build/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#I\.\./perl/#I\.\./\.#g' /build/vcftools-0.1.16/debian/vcftools/usr/share/doc/vcftools/examples/testsuite/test.t;
sed -i 's#\.\./perl/#/usr/bin/#g' /build/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/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
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/fill-rsIDs.1 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
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.1
man-recode --to-code UTF-8 --suffix .dh-new 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 debian/vcftools/usr/share/man/man1/vcf-merge.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
man-recode --to-code UTF-8 --suffix .dh-new debian/vcftools/usr/share/man/man1/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.1
man-recode --to-code UTF-8 --suffix .dh-new 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
mv debian/vcftools/usr/share/man/man1/vcf-validator.1.dh-new debian/vcftools/usr/share/man/man1/vcf-validator.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/vcf-validator.1 debian/vcftools/usr/share/man/man1/vcftools.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
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
chmod 0644 -- debian/vcftools/usr/share/man/man1/vcf-consensus.1 debian/vcftools/usr/share/man/man1/vcf-contrast.1 debian/vcftools/usr/share/man/man1/vcf-convert.1 debian/vcftools/usr/share/man/man1/vcf-fix-newlines.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
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
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
mv debian/vcftools/usr/share/man/man1/vcf-merge.1.dh-new debian/vcftools/usr/share/man/man1/vcf-merge.1
chmod 0644 -- 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 debian/vcftools/usr/share/man/man1/vcf-merge.1
mv debian/vcftools/usr/share/man/man1/fill-rsIDs.1.dh-new 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
chmod 0644 -- debian/vcftools/usr/share/man/man1/fill-rsIDs.1 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
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
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
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-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/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/be
objcopy --only-keep-debug --compress-debug-sections debian/vcftools/usr/bin/vcftools debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/be/125cba6e864edeb82bd5d332336945b59cbabd.debug
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/usr/lib/debug/.build-id/be/125cba6e864edeb82bd5d332336945b59cbabd.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/be/125cba6e864edeb82bd5d332336945b59cbabd.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
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 -Pdebian/.debhelper/vcftools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=vcftools-dbgsym "-DDepends=vcftools (= \${binary:Version})" "-DDescription=debug symbols for vcftools" -DBuild-Ids=be125cba6e864edeb82bd5d332336945b59cbabd -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/vcftools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pvcftools -ldebian/changelog -Tdebian/vcftools.substvars -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-dbgsym' in '../vcftools-dbgsym_0.1.16-3_arm64.deb'.
dpkg-deb: building package 'vcftools' in '../vcftools_0.1.16-3_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../vcftools_0.1.16-3_arm64.buildinfo
dpkg-genchanges --build=binary -O../vcftools_0.1.16-3_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/14261/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/14261/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/14261 and its subdirectories
I: Current time: Fri May 31 12:13:27 +14 2024
I: pbuilder-time-stamp: 1717107207