I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 3 20:11:00 +14 2025 I: pbuilder-time-stamp: 1738563060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [repeatmasker-recon_1.08-8.dsc] I: copying [./repeatmasker-recon_1.08.orig.tar.gz] I: copying [./repeatmasker-recon_1.08-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./repeatmasker-recon_1.08-8.dsc: unsupported subcommand dpkg-source: info: extracting repeatmasker-recon in repeatmasker-recon-1.08 dpkg-source: info: unpacking repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: unpacking repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-udpate-paths.patch dpkg-source: info: applying 0002-fix_binary_name.patch dpkg-source: info: applying 0003-hardening.patch dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 3 06:11 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=254c3df814364d85af63c9a885490579 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4025761 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.BsOKSXMy/pbuilderrc_J6E8 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BsOKSXMy/b2 --logfile b2/build.log repeatmasker-recon_1.08-8.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19920 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After unpacking 80.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Fetched 20.1 MB in 0s (180 MB/s) Preconfiguring packages ... 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 ... 19920 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-2_arm64.deb ... Unpacking bsdextrautils (2.40.4-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... 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%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... 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 (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/4025761/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j12 clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_autoreconf_clean -O--sourcedirectory=src debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' rm -rf bin dh_clean make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef In file included from imagespread.c:2: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from ele.h:1, from famdef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c: In function 'main': eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:246:7: note: in expansion of macro 'DUMBBELL' 246 | DUMBBELL; | ^~~~~~~~ eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:253:5: note: in expansion of macro 'DUMBBELL' 253 | DUMBBELL; | ^~~~~~~~ In file included from ele.h:1, from eleredef.c:5: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from ele.h:1, from edgeredef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eleredef.c: In function 'main': eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ edgeredef.c: In function 'general_edge_redef': edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | system(command); | ^~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' echo "Do not run tests since there exists no testsuite.sh needed to run those in the package" Do not run tests since there exists no testsuite.sh needed to run those in the package make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules execute_before_dh_auto_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' mkdir -p bin make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src cd src && make -j12 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_install -O--sourcedirectory=src debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_arm64.deb'. dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_arm64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4025761/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4025761/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/4025761 and its subdirectories I: Current time: Mon Feb 3 20:11:46 +14 2025 I: pbuilder-time-stamp: 1738563106