I: pbuilder: network access will be disabled during build
I: Current time: Thu Dec 19 05:37:05 +14 2024
I: pbuilder-time-stamp: 1734536225
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [libgkarrays_2.1.0+dfsg-4.2.dsc]
I: copying [./libgkarrays_2.1.0+dfsg.orig.tar.xz]
I: copying [./libgkarrays_2.1.0+dfsg-4.2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Feb 29 15:39:05 2024
gpgv: using RSA key A62D2CFBD50B9B5BF360D54B159EB5C4EFC8774C
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libgkarrays_2.1.0+dfsg-4.2.dsc: no acceptable signature found
dpkg-source: info: extracting libgkarrays in libgkarrays-2.1.0+dfsg
dpkg-source: info: unpacking libgkarrays_2.1.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking libgkarrays_2.1.0+dfsg-4.2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying proper_soname.patch
dpkg-source: info: applying fix_pkg-config.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/25267/tmp/hooks/D01_modify_environment starting
debug: Running on ff4a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Dec 18 15:37 /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/25267/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/25267/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=b419ea40991a49abbf821daa87e385ad
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=25267
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.dFk1utLj/pbuilderrc_33v2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dFk1utLj/b2 --logfile b2/build.log libgkarrays_2.1.0+dfsg-4.2.dsc'
SUDO_GID=113
SUDO_UID=107
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 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/25267/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 <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: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), d-shlibs (>= 0.106), 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 ... 19680 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 d-shlibs (>= 0.106); however:
Package d-shlibs 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} d-shlibs{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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} 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, 31 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.0 MB of archives. After unpacking 72.7 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-3 [195 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-3 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf d-shlibs all 0.108 [11.0 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.21 [88.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 23 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-3 [1488 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf debhelper all 13.21 [919 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Fetched 20.0 MB in 1s (13.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
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(Reading database ... 19680 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.22.5-3_armhf.deb ...
Unpacking gettext-base (0.22.5-3) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-6_armhf.deb ...
Unpacking groff-base (1.23.0-6) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-12_armhf.deb ...
Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ...
Unpacking man-db (2.13.0-1) ...
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_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.22.5-3_all.deb ...
Unpacking autopoint (0.22.5-3) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../15-d-shlibs_0.108_all.deb ...
Unpacking d-shlibs (0.108) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.21_all.deb ...
Unpacking libdebhelper-perl (13.21) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:armhf.
Preparing to unpack .../22-libelf1t64_0.192-4_armhf.deb ...
Unpacking libelf1t64:armhf (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ...
Unpacking dwz (0.15-1+b2) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-5+b1_armhf.deb ...
Unpacking libicu72:armhf (72.1-5+b1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ...
Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.22.5-3_armhf.deb ...
Unpacking gettext (0.22.5-3) ...
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_13.21_all.deb ...
Unpacking debhelper (13.21) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.21) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.22.5-3) ...
Setting up d-shlibs (0.108) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-3) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.21) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/25267/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/25267/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgkarrays_2.1.0+dfsg-4.2_source.changes
dpkg-buildpackage: info: source package libgkarrays
dpkg-buildpackage: info: source version 2.1.0+dfsg-4.2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Benjamin Drung <bdrung@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
aclocal: warning: couldn't open directory 'config/m4': No such file or directory
autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in'
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
aclocal: warning: couldn't open directory 'm4': No such file or directory
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:32: warning: The macro 'AM_PROG_LIBTOOL' is obsolete.
configure.in:32: You should run autoupdate.
m4/libtool.m4:101: AM_PROG_LIBTOOL is expanded from...
configure.in:32: the top level
configure.in:74: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.in:74: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.in:74: the top level
autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in'
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:32: installing './compile'
configure.in:32: installing './config.guess'
configure.in:32: installing './config.sub'
configure.in:31: installing './install-sh'
configure.in:31: installing './missing'
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
doc/Makefile.am:2: warning: suffix '.texinfo' for Texinfo files is discouraged; use '.texi' instead
doc/Makefile.am:2: installing 'doc/texinfo.tex'
libProgressBar/Makefile.am: installing './depcomp'
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'.
libtoolize: copying file 'config/m4/libtool.m4'
libtoolize: copying file 'config/m4/ltoptions.m4'
libtoolize: copying file 'config/m4/ltsugar.m4'
libtoolize: copying file 'config/m4/ltversion.m4'
libtoolize: copying file 'config/m4/lt~obsolete.m4'
configure.ac:213: installing 'config/compile'
configure.ac:231: installing 'config/config.guess'
configure.ac:231: installing 'config/config.sub'
configure.ac:206: installing 'config/install-sh'
configure.ac:206: installing 'config/missing'
doc/Makefile.am:107: installing 'config/texinfo.tex'
src/Makefile.am:117: warning: source file '$(SUX_DIR)/rank9b.cpp' is in a subdirectory,
src/Makefile.am:117: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least one source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am: installing 'config/depcomp'
tests/Makefile.am:125: warning: wildcard dataset/*.fa: non-POSIX variable name
tests/Makefile.am:125: (probably a GNU make extension)
parallel-tests: installing 'config/test-driver'
dh_auto_configure
./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
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 gawk... (cached) mawk
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 whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for texi2dvi... no
checking for pdftex... no
checking for kpsewhich... no
configure: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
configure: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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 dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for ld used by gcc... (cached) /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes
checking for dpkg... /usr/bin/dpkg
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/time.h... yes
checking for inline... inline
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for gettimeofday... yes
checking for memset... yes
checking for select... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99 or later... yes
checking for size_t... yes
checking for uint8_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for unsigned long long int... yes
checking for gzread in -lz... yes
checking for pthread_create in -lpthread... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating postinst
chmod: cannot access 'prerm': No such file or directory
config.status: creating prerm
config.status: creating control
config.status: creating libGkArrays.pc
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating src/sux/Makefile
config.status: creating src/kseq/Makefile
config.status: creating doc/Makefile
config.status: creating doc/libGkArrays.3
config.status: creating doc/package.texi
config.status: creating config/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in src/libProgressBar-1.2.0 (/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=arm-linux-gnueabihf' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/arm-linux-gnueabihf' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=arm-linux-gnueabihf' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=.
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 build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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 dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for dpkg... /usr/bin/dpkg
checking for rpmbuild... no
checking for rpm... no
checking for texi2dvi... no
checking for pdftex... no
checking for kpsewhich... no
configure: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
configure: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for sys/mkdev.h... no
checking for sys/sysmacros.h... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct stat.st_blocks... yes
checking whether ln -s works... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for sys/time.h... yes
checking for time.h... yes
checking for sys/sysmacros.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for memory.h... yes
checking for fcntl.h... yes
checking for alloca.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating postinst
chmod: cannot access 'prerm': No such file or directory
config.status: creating prerm
config.status: creating libProgressBar.lsm
config.status: creating libProgressBar.spec
config.status: creating control
config.status: creating libProgressBar.pc
config.status: creating Makefile
config.status: creating libProgressBar/Makefile
config.status: creating doc/Makefile
config.status: creating doc/libProgressBar.3
config.status: creating libProgressBar/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build
make -j4
make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
Making all in src
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
Making all in kseq
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
Making all in sux
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
Making all in libProgressBar-1.2.0
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
Making all in libProgressBar
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make all-am
make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
g++ -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o testPB.o testPB.cpp
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -fPIC -DPIC -o .libs/progressBar.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -o progressBar.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/arm-linux-gnueabihf progressBar.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/14/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/arm-linux-gnueabihf/14 -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/14/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crtn.o -O6 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libProgressBar.so.0 -o .libs/libProgressBar.so.0.1.2
libtool: link: (cd ".libs" && rm -f "libProgressBar.so.0" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so.0")
libtool: link: (cd ".libs" && rm -f "libProgressBar.so" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so")
libtool: link: ar cr .libs/libProgressBar.a progressBar.o
libtool: link: ranlib .libs/libProgressBar.a
libtool: link: ( cd ".libs" && rm -f "libProgressBar.la" && ln -s "../libProgressBar.la" "libProgressBar.la" )
/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -lProgressBar -Wl,-z,relro -Wl,-z,now -o testProgressBar testPB.o libProgressBar.la
libtool: link: g++ -O6 -Wall --pedantic --ansi -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testProgressBar testPB.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libProgressBar.so
make[5]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
cp "libProgressBar.pc" "libProgressBar-1.2.0.pc"
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o buildTables.o buildTables.cpp
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gkArrays.lo gkArrays.cpp
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o solArray.lo solArray.cpp
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o utils.lo utils.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c utils.cpp -fPIC -DPIC -o .libs/utils.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkArrays.cpp -fPIC -DPIC -o .libs/gkArrays.o
In file included from ./readsReader.h:109,
from ./gkArrays.h:115,
from buildTables.cpp:111:
./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1
In file included from readsReader.h:109,
from gkArrays.h:115,
from gkArrays.cpp:113:
kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gkArraysBuilder.lo gkArraysBuilder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.o
gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTagFactor(uint, uint, uint)':
gkArrays.cpp:454:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation]
454 | strncpy(&final_dna[previous_length], dna, 4);
| ^
gkArrays.cpp:460:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation]
460 | strncpy(&final_dna[previous_length], dna, (p+fact_length+readPos)%4);
| ^
gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTag(uint)':
gkArrays.cpp:425:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation]
425 | strncpy(&final_dna[previous_length], dna, 4);
| ^
gkArrays.cpp:430:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation]
430 | strncpy(&final_dna[previous_length], dna, nextReadPos%4);
| ^
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.o
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp
In file included from readsReader.h:109,
from gkArrays.h:115,
from gkArraysBuilder.h:105,
from gkArraysBuilder.cpp:103:
kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1
gkSABuilder.cpp: In function 'int64_t gkarrays::partition(SolArray*, SolArray*, uintSA, uintSA, uintSA)':
gkSABuilder.cpp:340:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
340 | while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i))));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./readsReader.h:109,
from ./gkArrays.h:115,
from ./gkSABuilder.h:108,
from gkSABuilder.cpp:104:
./readsReader.h: At global scope:
./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from readsReader.h:109,
from gkArrays.h:115,
from gkCFPSBuilder.cpp:110:
kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkIFABuilder.cpp -fPIC -DPIC -o .libs/gkIFABuilder.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -o gkCFPSBuilder.o >/dev/null 2>&1
In file included from ./readsReader.h:109,
from ./gkArrays.h:115,
from ./gkIFABuilder.h:107,
from gkIFABuilder.cpp:105:
./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkIFABuilder.cpp -o gkIFABuilder.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o readsReader.lo readsReader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o largebinvect.lo largebinvect.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c largebinvect.cxx -fPIC -DPIC -o .libs/largebinvect.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o bitvector.lo bitvector.cxx
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rank9b.lo `test -f 'sux/rank9b.cpp' || echo './'`sux/rank9b.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c readsReader.cpp -o readsReader.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1
sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)':
sux/rank9b.cpp:144:100: warning: suggest parentheses around '-' inside '>>' [-Wparentheses]
144 | return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) );
| ~~~~~~~~~~~~~~~~~~^~~
sux/rank9b.cpp: In member function 'uint64_t rank9b::select(uint64_t)':
sux/rank9b.cpp:207:88: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
207 | const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF );
| ~~~~~~~~~~~~~~~~^~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/arm-linux-gnueabihf gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/14/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -Wl,-rpath -Wl,/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so -lpthread -lz -L/usr/lib/gcc/arm-linux-gnueabihf/14 -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/14/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0
libtool: link: (cd ".libs" && rm -f "libGkArrays.so.1" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so.1")
libtool: link: (cd ".libs" && rm -f "libGkArrays.so" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so")
libtool: link: ar cr .libs/libGkArrays.a gkArrays.o solArray.o utils.o gkArraysBuilder.o gkSABuilder.o gkCFPSBuilder.o gkIFABuilder.o readsReader.o largebinvect.o bitvector.o rank9b.o
libtool: link: ranlib .libs/libGkArrays.a
libtool: link: ( cd ".libs" && rm -f "libGkArrays.la" && ln -s "../libGkArrays.la" "libGkArrays.la" )
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/buildTables buildTables.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libGkArrays.so -lpthread -lz
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
Making all in tests
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
cp "libGkArrays.pc" "libGkArrays-2.1.0.pc"
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[1]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
dh_auto_test
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
Making check in src
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
Making check in kseq
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make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
Making check in sux
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
Making check in libProgressBar-1.2.0
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
Making check in libProgressBar
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make[4]: Nothing to be done for 'check-am'.
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Making check in tests
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make variableAndFixedLength testPairedEnd testVariableFixed testConsistency
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o variableAndFixedLength.o variableAndFixedLength.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o compareVariableFixed.o compareVariableFixed.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o testPairedEnd.o testPairedEnd.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o checkPairedEnd.o checkPairedEnd.cpp
In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109,
from checkPairedEnd.cpp:104:
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109,
from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115,
from compareVariableFixed.cpp:109:
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o testVariableFixed.o testVariableFixed.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o testConsistency.o testConsistency.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o checkConsistency.o checkConsistency.cpp
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz
In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109,
from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115,
from checkConsistency.cpp:104:
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testPairedEnd testPairedEnd.o checkPairedEnd.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testVariableFixed testVariableFixed.o compareVariableFixed.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz
/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz
libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testConsistency testConsistency.o checkConsistency.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make check-TESTS
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
PASS: testPairedEnd
PASS: testVariableFixed
PASS: testConsistency
============================================================================
Testsuite summary for libGkArrays 2.1.0
============================================================================
# TOTAL: 3
# PASS: 3
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
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create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j1 install DESTDIR=/build/reproducible-path/libgkarrays-2.1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
Making install in src
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
Making install in kseq
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
make[4]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq'
/usr/bin/install -c -m 644 kseq.h '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq'
Making install in sux
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
make[4]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux'
/usr/bin/install -c -m 644 macros.h popcount.h rank9b.h '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/sux'
Making install in libProgressBar-1.2.0
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
Making install in libProgressBar
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/sh ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar.so.0.1.2
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so.0 || { rm -f libProgressBar.so.0 && ln -s libProgressBar.so.0.1.2 libProgressBar.so.0; }; })
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so || { rm -f libProgressBar.so && ln -s libProgressBar.so.0.1.2 libProgressBar.so; }; })
libtool: install: /usr/bin/install -c .libs/libProgressBar.lai /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar.la
libtool: install: /usr/bin/install -c .libs/libProgressBar.a /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar.a
libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar.a
libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar-1.2.0/include'
/usr/bin/install -c -m 644 config.h '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libProgressBar-1.2.0/include'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0'
/usr/bin/install -c -m 644 progressBar.h '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0'
make install-data-hook
make[6]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
ln -s -f libProgressBar-1.2.0 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar
make[6]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[5]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[5]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 libProgressBar-1.2.0.pc '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make install-data-hook
make[6]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
ln -s -f libProgressBar-1.2.0.pc /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/libProgressBar.pc
make[6]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[5]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0'
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/sh ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: warning: relinking 'libGkArrays.la'
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/src; /bin/sh "/build/reproducible-path/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/arm-linux-gnueabihf gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/14/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lProgressBar -lpthread -lz -L/usr/lib/gcc/arm-linux-gnueabihf/14 -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/14/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/14/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/14/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0
libtool: install: /usr/bin/install -c .libs/libGkArrays.so.1.1.0T /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.so.1.1.0
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so.1 || { rm -f libGkArrays.so.1 && ln -s libGkArrays.so.1.1.0 libGkArrays.so.1; }; })
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so || { rm -f libGkArrays.so && ln -s libGkArrays.so.1.1.0 libGkArrays.so; }; })
libtool: install: /usr/bin/install -c .libs/libGkArrays.lai /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.la
libtool: install: /usr/bin/install -c .libs/libGkArrays.a /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.a
libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.a
libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0'
/usr/bin/install -c -m 644 gkArrays.h solArray.h gkArraysTypes.h gkArraysBuilder.h gkSABuilder.h gkCFPSBuilder.h gkIFABuilder.h readsReader.h bitvector.hxx largebinvect.hxx bitvector.cxx largebinvect.cxx binvect.hxx '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays-2.1.0/include'
/usr/bin/install -c -m 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/config/config.h '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays-2.1.0/include'
make install-data-hook
make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
ln -s -f libGkArrays-2.1.0 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays
make[5]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src'
Making install in tests
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
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/libgkarrays-2.1.0+dfsg/tests'
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests'
make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 libGkArrays-2.1.0.pc '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make install-data-hook
make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
ln -s -f libGkArrays-2.1.0.pc /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/libGkArrays.pc
make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
make[1]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
dh_install
d-shlibmove --commit \
--t64 \
--multiarch \
--devunversioned \
--exclude-la \
--override s/libProgressBar0-dev// \
--movedev debian/tmp/usr/include usr \
--movedev debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig usr/lib/arm-linux-gnueabihf \
debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libgkarrays-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libgkarrays1t64/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.a debian/libgkarrays-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.so debian/libgkarrays-dev/usr/lib/arm-linux-gnueabihf
mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.so.1 debian/libgkarrays1t64/usr/lib/arm-linux-gnueabihf
mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libGkArrays.so.1.1.0 debian/libgkarrays1t64/usr/lib/arm-linux-gnueabihf
PKGDEV=libgkarrays-dev
PKGSHL=libgkarrays1t64
install -d -m 755 debian/libgkarrays-dev/usr
mv debian/tmp/usr/include debian/libgkarrays-dev/usr
install -d -m 755 debian/libgkarrays-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig debian/libgkarrays-dev/usr/lib/arm-linux-gnueabihf
# now move libProgressBar manually
dh_install -p libgkarrays1t64 usr/lib/arm-linux-gnueabihf/libProgressBar.so.0* usr/lib/arm-linux-gnueabihf
chmod -x debian/*/usr/lib/arm-linux-gnueabihf/libProgressBar.so.0.*
dh_install -p libgkarrays-dev usr/lib/arm-linux-gnueabihf/libProgressBar.so usr/lib/arm-linux-gnueabihf
dh_install -p libgkarrays-dev usr/lib/arm-linux-gnueabihf/libProgressBar.a usr/lib/arm-linux-gnueabihf
dh_install -p libgkarrays-dev usr/lib/arm-linux-gnueabihf/libGkArrays-2.1.0/include/* usr/include/libGkArrays-2.1.0
dh_install -p libgkarrays-dev usr/lib/arm-linux-gnueabihf/libProgressBar-1.2.0/include/* usr/include/libProgressBar-1.2.0
find debian/tmp -name "lib*.la" -delete
make[1]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
dh_installdocs
dh_installchangelogs
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dwz: debian/libgkarrays1t64/usr/lib/arm-linux-gnueabihf/libProgressBar.so.0.1.2: .debug_info section not present
dwz: Too few files for multifile optimization
dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it.
dh_dwz: warning: Common issues include no debug information at all (missing -g) and
dh_dwz: warning: compressed debug information (#931891).
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libgkarrays-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: package libgkarrays-dev: substitution variable ${devlibs:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'libgkarrays1t64' in '../libgkarrays1t64_2.1.0+dfsg-4.2_armhf.deb'.
dpkg-deb: building package 'libgkarrays1t64-dbgsym' in '../libgkarrays1t64-dbgsym_2.1.0+dfsg-4.2_armhf.deb'.
dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-4.2_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_armhf.buildinfo
dpkg-genchanges --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_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/25267/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/25267/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/25267 and its subdirectories
I: Current time: Thu Dec 19 05:40:05 +14 2024
I: pbuilder-time-stamp: 1734536405