I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 25 15:44:36 +14 2024 I: pbuilder-time-stamp: 1729820676 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 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/38921/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 25 01:45 /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/38921/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/38921/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4cd0aa8648184ccc846169992018d3c6 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=38921 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.tChQb2hb/pbuilderrc_jK7T --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tChQb2hb/b2 --logfile b2/build.log libgkarrays_2.1.0+dfsg-4.2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/38921/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 21880 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 20.7 MB of archives. After unpacking 76.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.107 [11.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Fetched 20.7 MB in 3s (7345 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21880 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_amd64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.107_all.deb ... Unpacking d-shlibs (0.107) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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:amd64. Preparing to unpack .../22-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.107) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... 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 (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/38921/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/38921/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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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=x86_64-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/x86_64-linux-gnu --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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-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 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 -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) 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=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=x86_64-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 -fcf-protection' '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 -fcf-protection' --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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-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 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 -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) 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 -j20 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/sh ../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/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/x86_64-linux-gnu progressBar.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-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/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/ -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 -fcf-protection -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/ -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 -fcf-protection -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/ -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 -fcf-protection -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/ -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 -fcf-protection -c -o utils.lo utils.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/ -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 -fcf-protection -c -o gkArraysBuilder.lo gkArraysBuilder.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/ -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 -fcf-protection -c -o gkSABuilder.lo gkSABuilder.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/ -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 -fcf-protection -c -o gkCFPSBuilder.lo gkCFPSBuilder.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/ -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 -fcf-protection -c -o gkIFABuilder.lo gkIFABuilder.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/ -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 -fcf-protection -c -o readsReader.lo readsReader.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/ -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 -fcf-protection -c -o largebinvect.lo largebinvect.cxx /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/ -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 -fcf-protection -c -o bitvector.lo bitvector.cxx /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/ -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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/ -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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) | ^~~~~~~~~ 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 -fcf-protection -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 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) | ^~~~~~~~~ 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) | ^~~~~~~~~ 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 -fcf-protection -c gkArraysBuilder.cpp -o gkArraysBuilder.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/ -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 -fcf-protection -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 -fcf-protection -c utils.cpp -o utils.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) | ^~~~~~~~~ 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 -fcf-protection -c largebinvect.cxx -o largebinvect.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 -fcf-protection -c solArray.cpp -o solArray.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) | ^~~~~~~~~ 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); | ^ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c gkSABuilder.cpp -o gkSABuilder.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 -fcf-protection -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/x86_64-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/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-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/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/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 -fcf-protection -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 -fcf-protection -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 -j20 check "TESTSUITEFLAGS=-j20 --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 make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/kseq' make[3]: Nothing to be done for 'check'. 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 make[4]: Entering 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[4]: Nothing to be done for 'check-am'. 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[3]: Nothing to be done for 'check-am'. 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 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=\"./\" -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o checkConsistency.o checkConsistency.cpp 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) | ^~~~~~~~~ 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) | ^~~~~~~~~ /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 -fcf-protection -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/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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 /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 -fcf-protection -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 -fcf-protection -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' 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[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' 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/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-linux-gnu/libProgressBar.so.0.1.2 libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/libProgressBar.a libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.a libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' 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 -fcf-protection -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/x86_64-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/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-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/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/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/x86_64-linux-gnu/libGkArrays.so.1.1.0 libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/libGkArrays.a libtool: install: chmod 644 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a libtool: install: ranlib /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/pkgconfig usr/lib/x86_64-linux-gnu \ debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libgkarrays1t64/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so.1 debian/libgkarrays1t64/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so.1.1.0 debian/libgkarrays1t64/usr/lib/x86_64-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/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu # now move libProgressBar manually dh_install -p libgkarrays1t64 usr/lib/x86_64-linux-gnu/libProgressBar.so.0* usr/lib/x86_64-linux-gnu chmod -x debian/*/usr/lib/x86_64-linux-gnu/libProgressBar.so.0.* dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libProgressBar.so usr/lib/x86_64-linux-gnu dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libProgressBar.a usr/lib/x86_64-linux-gnu dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libGkArrays-2.1.0/include/* usr/include/libGkArrays-2.1.0 dh_install -p libgkarrays-dev usr/lib/x86_64-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/x86_64-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 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_amd64.deb'. dpkg-deb: building package 'libgkarrays1t64-dbgsym' in '../libgkarrays1t64-dbgsym_2.1.0+dfsg-4.2_amd64.deb'. dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-4.2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_amd64.buildinfo dpkg-genchanges --build=binary -O../libgkarrays_2.1.0+dfsg-4.2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/38921/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/38921/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/38921 and its subdirectories I: Current time: Fri Oct 25 15:48:52 +14 2024 I: pbuilder-time-stamp: 1729820932