Sat Mar 8 07:51:23 UTC 2025 I: starting to build libgkarrays/trixie/arm64 on jenkins on '2025-03-08 07:51'
Sat Mar 8 07:51:23 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/60453/console.log
Sat Mar 8 07:51:23 UTC 2025 I: Downloading source for trixie/libgkarrays=2.1.0+dfsg-4.2
--2025-03-08 07:51:23-- http://deb.debian.org/debian/pool/main/libg/libgkarrays/libgkarrays_2.1.0%2bdfsg-4.2.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2115 (2.1K) [text/prs.lines.tag]
Saving to: ‘libgkarrays_2.1.0+dfsg-4.2.dsc’
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2025-03-08 07:51:23 (211 MB/s) - ‘libgkarrays_2.1.0+dfsg-4.2.dsc’ saved [2115/2115]
Sat Mar 8 07:51:23 UTC 2025 I: libgkarrays_2.1.0+dfsg-4.2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: libgkarrays
Binary: libgkarrays1t64, libgkarrays-dev
Architecture: any
Version: 2.1.0+dfsg-4.2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://crac.gforge.inria.fr/gkarrays/
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libgkarrays
Vcs-Git: https://salsa.debian.org/med-team/libgkarrays.git
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), d-shlibs (>= 0.106), zlib1g-dev
Package-List:
libgkarrays-dev deb libdevel optional arch=any
libgkarrays1t64 deb libs optional arch=any
Checksums-Sha1:
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Files:
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Sat Mar 8 07:51:23 UTC 2025 I: Checking whether the package is not for us
Sat Mar 8 07:51:23 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net.
Sat Mar 8 07:51:23 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net.
Sat Mar 8 07:52:34 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Mar 7 19:51:26 -12 2025
I: pbuilder-time-stamp: 1741420286
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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
dpkg-source: warning: cannot verify inline signature for ./libgkarrays_2.1.0+dfsg-4.2.dsc: unsupported subcommand
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/3706214/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='b055654e3f154a7d9b4e5b17a449ad73'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3706214'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/pbuilderrc_QzwT --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/b1 --logfile b1/build.log libgkarrays_2.1.0+dfsg-4.2.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3706214/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: 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 ... 19914 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} libunistring5{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, 32 newly installed, 0 to remove and 0 not upgraded.
Need to get 21.0 MB of archives. After unpacking 81.6 MB will be used.
Writing extended state information...
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Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
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Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB]
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Get: 16 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Fetched 21.0 MB in 0s (141 MB/s)
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(Reading database ... 19914 files and directories currently installed.)
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Setting up libpipeline1:arm64 (1.5.8-1) ...
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update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
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Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 arm64
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 incompatibility.
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=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
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checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... 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
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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
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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... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
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
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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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
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checking how to recognize dependent libraries... pass_all
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checking how to associate runtime and link libraries... printf %s\n
checking for ranlib... ranlib
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
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checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
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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
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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
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checking for GNU libc compatible malloc... yes
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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/bash ./configure --disable-option-checking '--prefix=/usr' '--build=aarch64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/aarch64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=aarch64-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-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 -mbranch-protection=standard' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
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 xargs -n works... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu 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 ranlib... ranlib
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
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 -j12
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. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o testPB.o testPB.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -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. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -o progressBar.o >/dev/null 2>&1
/bin/bash ../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/aarch64-linux-gnu progressBar.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/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/bash ../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/ -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 -mbranch-protection=standard -c -o buildTables.o buildTables.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o gkArrays.lo gkArrays.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o solArray.lo solArray.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o utils.lo utils.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o gkArraysBuilder.lo gkArraysBuilder.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o gkSABuilder.lo gkSABuilder.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o gkIFABuilder.lo gkIFABuilder.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o readsReader.lo readsReader.cpp
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o largebinvect.lo largebinvect.cxx
/bin/bash ../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/ -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 -mbranch-protection=standard -c -o bitvector.lo bitvector.cxx
/bin/bash ../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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c gkArrays.cpp -fPIC -DPIC -o .libs/gkArrays.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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.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/ -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 -mbranch-protection=standard -c utils.cpp -fPIC -DPIC -o .libs/utils.o
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/ -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 -mbranch-protection=standard -c largebinvect.cxx -o largebinvect.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 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)
| ^~~~~~~~~
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/ -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 -mbranch-protection=standard -c sux/rank9b.cpp -o rank9b.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/ -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 -mbranch-protection=standard -c gkArraysBuilder.cpp -o gkArraysBuilder.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/ -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 -mbranch-protection=standard -c bitvector.cxx -o bitvector.o >/dev/null 2>&1
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)
| ^~~~~~~~~
gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTagFactor(uint, uint, uint)':
gkArrays.cpp:454:14: warning: 'char* __builtin_strncpy(char*, const char*, long 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*, long 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);
| ^
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/ -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 -mbranch-protection=standard -c utils.cpp -o utils.o >/dev/null 2>&1
gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTag(uint)':
gkArrays.cpp:425:14: warning: 'char* __builtin_strncpy(char*, const char*, long 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*, long 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);
| ^
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/ -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 -mbranch-protection=standard -c solArray.cpp -o solArray.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/ -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 -mbranch-protection=standard -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/ -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 -mbranch-protection=standard -c gkIFABuilder.cpp -o gkIFABuilder.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/ -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 -mbranch-protection=standard -c gkCFPSBuilder.cpp -o gkCFPSBuilder.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/ -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 -mbranch-protection=standard -c gkArrays.cpp -o gkArrays.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/ -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 -mbranch-protection=standard -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1
/bin/bash ../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 -mbranch-protection=standard -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/aarch64-linux-gnu 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/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/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -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/bash ../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 -mbranch-protection=standard -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 -mbranch-protection=standard -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'
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make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
cp "libGkArrays.pc" "libGkArrays-2.1.0.pc"
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dh_auto_test
make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg'
Making check in src
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Making check in kseq
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Making check in sux
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Making check in libProgressBar-1.2.0
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Making check in libProgressBar
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Making check in tests
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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=\"./\" -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 -mbranch-protection=standard -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=\"./\" -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 -mbranch-protection=standard -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=\"./\" -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 -mbranch-protection=standard -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=\"./\" -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 -mbranch-protection=standard -c -o checkPairedEnd.o checkPairedEnd.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -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 -mbranch-protection=standard -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=\"./\" -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 -mbranch-protection=standard -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=\"./\" -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 -mbranch-protection=standard -c -o checkConsistency.o checkConsistency.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)
| ^~~~~~~~~
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/bash ../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 -mbranch-protection=standard -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
/bin/bash ../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 -mbranch-protection=standard -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/bash ../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 -mbranch-protection=standard -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 -mbranch-protection=standard -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
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 -mbranch-protection=standard -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
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/bin/bash ../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 -mbranch-protection=standard -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
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make check-TESTS
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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
============================================================================
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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/aarch64-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libProgressBar.so.0.1.2
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { 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/aarch64-linux-gnu && { 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/aarch64-linux-gnu/libProgressBar.la
libtool: install: /usr/bin/install -c .libs/libProgressBar.a /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libProgressBar.a
libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libProgressBar.a
libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libProgressBar.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/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/aarch64-linux-gnu/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/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 libProgressBar-1.2.0.pc '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/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/aarch64-linux-gnu/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/aarch64-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: warning: relinking 'libGkArrays.la'
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/src; /bin/bash "/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 -mbranch-protection=standard -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/aarch64-linux-gnu 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/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/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/libGkArrays.so.1.1.0
libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { 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/aarch64-linux-gnu && { 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/aarch64-linux-gnu/libGkArrays.la
libtool: install: /usr/bin/install -c .libs/libGkArrays.a /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.a
libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.a
libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/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/aarch64-linux-gnu/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/aarch64-linux-gnu/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/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 libGkArrays-2.1.0.pc '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/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/aarch64-linux-gnu/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/aarch64-linux-gnu/pkgconfig usr/lib/aarch64-linux-gnu \
debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libgkarrays-dev/usr/lib/aarch64-linux-gnu
install -d -m 755 debian/libgkarrays1t64/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.a debian/libgkarrays-dev/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.so debian/libgkarrays-dev/usr/lib/aarch64-linux-gnu
mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.so.1 debian/libgkarrays1t64/usr/lib/aarch64-linux-gnu
mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.so.1.1.0 debian/libgkarrays1t64/usr/lib/aarch64-linux-gnu
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/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig debian/libgkarrays-dev/usr/lib/aarch64-linux-gnu
# now move libProgressBar manually
dh_install -p libgkarrays1t64 usr/lib/aarch64-linux-gnu/libProgressBar.so.0* usr/lib/aarch64-linux-gnu
chmod -x debian/*/usr/lib/aarch64-linux-gnu/libProgressBar.so.0.*
dh_install -p libgkarrays-dev usr/lib/aarch64-linux-gnu/libProgressBar.so usr/lib/aarch64-linux-gnu
dh_install -p libgkarrays-dev usr/lib/aarch64-linux-gnu/libProgressBar.a usr/lib/aarch64-linux-gnu
dh_install -p libgkarrays-dev usr/lib/aarch64-linux-gnu/libGkArrays-2.1.0/include/* usr/include/libGkArrays-2.1.0
dh_install -p libgkarrays-dev usr/lib/aarch64-linux-gnu/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/aarch64-linux-gnu/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-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.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_arm64.deb'.
dpkg-deb: building package 'libgkarrays1t64-dbgsym' in '../libgkarrays1t64-dbgsym_2.1.0+dfsg-4.2_arm64.deb'.
dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-4.2_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo
dpkg-genchanges --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/3706214 and its subdirectories
I: Current time: Fri Mar 7 19:52:33 -12 2025
I: pbuilder-time-stamp: 1741420353
Sat Mar 8 07:52:35 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net.
Sat Mar 8 07:52:35 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net.
Sat Mar 8 07:53:54 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
Sat Mar 8 07:53:54 UTC 2025 I: libgkarrays_2.1.0+dfsg-4.2_arm64.changes:
Format: 1.8
Date: Wed, 28 Feb 2024 18:55:49 +0000
Source: libgkarrays
Binary: libgkarrays-dev libgkarrays1t64 libgkarrays1t64-dbgsym
Architecture: arm64
Version: 2.1.0+dfsg-4.2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Benjamin Drung <bdrung@debian.org>
Description:
libgkarrays-dev - library to query large collection of NGS sequences (development)
libgkarrays1t64 - library to query large collection of NGS sequences
Closes: 1062316
Changes:
libgkarrays (2.1.0+dfsg-4.2) unstable; urgency=medium
.
* Non-maintainer upload.
* Rename libraries for 64-bit time_t transition. Closes: #1062316
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7d28ca441f07e93a82d476a05d7afc68bf57769f09503d47e3ce7214d4af2fc1 182412 libgkarrays1t64-dbgsym_2.1.0+dfsg-4.2_arm64.deb
96e3d5805993d3ac1822f80c8e207121d161f6c464f991e76eb2b54f77d77afe 54052 libgkarrays1t64_2.1.0+dfsg-4.2_arm64.deb
ce58bb99446fce54771493a6f9278a89fe4bfe1f335b4019c66fda3b101061f2 5714 libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo
Files:
a13caa26273a70da0dd0ff4266a34ba1 83124 libdevel optional libgkarrays-dev_2.1.0+dfsg-4.2_arm64.deb
7947b5c46ee0cc5348e35d0066b1a9d5 182412 debug optional libgkarrays1t64-dbgsym_2.1.0+dfsg-4.2_arm64.deb
d7d350f6771ff3313df2b8bb94292e9d 54052 libs optional libgkarrays1t64_2.1.0+dfsg-4.2_arm64.deb
bb4430f14b0d845fd2395ad655afc91b 5714 science optional libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo
Sat Mar 8 07:53:56 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_7-60453.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/libgkarrays_2.1.0+dfsg-4.2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/libgkarrays_2.1.0+dfsg-4.2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/libgkarrays_2.1.0+dfsg-4.2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/b1/libgkarrays_2.1.0+dfsg-4.2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.XgTWAPFB/b2/libgkarrays_2.1.0+dfsg-4.2_arm64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 236ms
CPU time consumed: 233ms
Sat Mar 8 07:53:56 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sat Mar 8 07:53:56 UTC 2025 I: libgkarrays from trixie built successfully and reproducibly on arm64.
Sat Mar 8 07:53:57 UTC 2025 I: Submitting .buildinfo files to external archives:
Sat Mar 8 07:53:57 UTC 2025 I: Submitting 8.0K b1/libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo.asc
Sat Mar 8 07:54:21 UTC 2025 I: Submitting 8.0K b2/libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo.asc
Sat Mar 8 07:54:39 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Mar 8 07:54:39 UTC 2025 I: Done submitting .buildinfo files.
Sat Mar 8 07:54:39 UTC 2025 I: Removing signed libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo.asc files:
removed './b1/libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo.asc'
removed './b2/libgkarrays_2.1.0+dfsg-4.2_arm64.buildinfo.asc'