Running as unit: rb-build-arm64_10-45493.service ==================================================================================== Thu Nov 21 22:01:51 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_10) on jenkins, called using "codethink04-arm64 codethink02-arm64" as arguments. Thu Nov 21 22:01:51 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-KkOtZ8Kh" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:01:52 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 22:01:52 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-cfhJpD' Thu Nov 21 22:01:52 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Thu Nov 21 22:01:52 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-gAjXDD' ok, let's check if lagan is building anywhere yet… ok, lagan is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of lagan in trixie on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink02-arm64.debian.net. ============================================================================= Thu Nov 21 22:01:58 UTC 2024 I: starting to build lagan/trixie/arm64 on jenkins on '2024-11-21 22:01' Thu Nov 21 22:01:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/45493/console.log 1732226518 arm64 trixie lagan Thu Nov 21 22:01:58 UTC 2024 I: Downloading source for trixie/lagan=2.0-10 --2024-11-21 22:01:59-- http://deb.debian.org/debian/pool/main/l/lagan/lagan_2.0-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1354 (1.3K) [text/prs.lines.tag] Saving to: ‘lagan_2.0-10.dsc’ 0K . 100% 177M=0s 2024-11-21 22:01:59 (177 MB/s) - ‘lagan_2.0-10.dsc’ saved [1354/1354] --2024-11-21 22:01:59-- http://deb.debian.org/debian/pool/main/l/lagan/lagan_2.0-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1354 (1.3K) [text/prs.lines.tag] Saving to: ‘lagan_2.0-10.dsc’ 0K . 100% 177M=0s 2024-11-21 22:01:59 (177 MB/s) - ‘lagan_2.0-10.dsc’ saved [1354/1354] Thu Nov 21 22:01:59 UTC 2024 I: lagan_2.0-10.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: lagan Binary: lagan Architecture: any Version: 2.0-10 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Steffen Moeller Homepage: http://lagan.stanford.edu/lagan_web/index.shtml Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/lagan Vcs-Git: https://salsa.debian.org/med-team/lagan.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libboost-dev Package-List: lagan deb science optional arch=any Checksums-Sha1: 2417bec99ff59541287ad56fdfe3abb609323949 192945 lagan_2.0.orig.tar.gz 54fa9631bdac105245aaf917f96951ddd7396770 10268 lagan_2.0-10.debian.tar.xz Checksums-Sha256: 9e3c27d0fd7a3f3448035ea51996a50e314b139942d9313858c3e4678aae1281 192945 lagan_2.0.orig.tar.gz ccec357e8c330b4f546dcfbd1608d58e1488e8e361bd444d70c020d4ff3d45bc 10268 lagan_2.0-10.debian.tar.xz Files: 7027ba63a2a5115871b85e205aa36bb7 192945 lagan_2.0.orig.tar.gz 981c1cb44dce36fbdb1f6f444885e419 10268 lagan_2.0-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCZgEibQAKCRAqJ5BL1yQ+ 2gtPAQCBqTHH0AstiYMa8H2MUveTjKHZwZ5y/LBZH14RqkRWpQD8DnT2VTMNUzUy BuTkwSLIK2kNcSDSRnhyKU8Wmzm9pQI= =LuI8 -----END PGP SIGNATURE----- Thu Nov 21 22:01:59 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 22:01:59 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Nov 21 22:01:59 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Nov 21 22:01:59 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 22:01:59 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ZiLHzE' ==================================================================================== Thu Nov 21 22:02:00 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 lagan trixie /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY 2.0-10" as arguments. Thu Nov 21 22:02:00 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-sbbO0T3P" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:02:00 UTC 2024 I: Downloading source for trixie/lagan=2.0-10 Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (15.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (15.5 MB/s) Download complete and in download only mode ============================================================================= Building lagan in trixie on arm64 on codethink04-arm64 now. Date: Thu Nov 21 22:02:01 GMT 2024 Date UTC: Thu Nov 21 22:02:01 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 10:02:01 -12 2024 I: pbuilder-time-stamp: 1732226521 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 [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/555636/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0de0fe0ad1e64771bd1e734d65a843e4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='555636' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/pbuilderrc_pE10 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/555636/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), libboost-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 ... 20087 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{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} 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 30.0 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Fetched 30.0 MB in 0s (176 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 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_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_arm64.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 libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-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 .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../29-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../30-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libboost1.83-dev:arm64 (1.83.0-3.2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... 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 libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/lagan-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro anchors.c: In function 'anchors_getline': anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro order.c: In function 'readfile': order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'readseq': utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_arm64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_arm64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/555636 and its subdirectories I: Current time: Thu Nov 21 10:02:35 -12 2024 I: pbuilder-time-stamp: 1732226555 Thu Nov 21 22:02:35 UTC 2024 I: Signing ./b1/lagan_2.0-10_arm64.buildinfo as lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:02:36 UTC 2024 I: Signed ./b1/lagan_2.0-10_arm64.buildinfo as ./b1/lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:02:36 UTC 2024 - build #1 for lagan/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 22:02:36 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-sbbO0T3P, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:01 b2 -rw-r--r-- 1 jenkins jenkins 1354 Mar 25 2024 lagan_2.0-10.dsc -rw------- 1 jenkins jenkins 2441 Nov 21 22:01 rbuildlog.2SZKOWb /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1: total 1096 -rw-r--r-- 1 jenkins jenkins 51700 Nov 21 22:02 build.log -rw-r--r-- 1 jenkins jenkins 846460 Nov 21 22:02 lagan-dbgsym_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 10268 Nov 21 22:02 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Nov 21 22:02 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4977 Nov 21 22:02 lagan_2.0-10_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5859 Nov 21 22:02 lagan_2.0-10_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Nov 21 22:02 lagan_2.0-10_arm64.changes -rw-r--r-- 1 jenkins jenkins 177036 Nov 21 22:02 lagan_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 1225 Nov 21 22:02 lagan_2.0-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b2: total 0 Thu Nov 21 22:02:37 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 10:02:01 -12 2024 I: pbuilder-time-stamp: 1732226521 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 [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/555636/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0de0fe0ad1e64771bd1e734d65a843e4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='555636' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/pbuilderrc_pE10 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/555636/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), libboost-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 ... 20087 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{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} 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 30.0 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Fetched 30.0 MB in 0s (176 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 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_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_arm64.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 libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-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 .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../29-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../30-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libboost1.83-dev:arm64 (1.83.0-3.2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... 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 libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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: Running cd /build/reproducible-path/lagan-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro anchors.c: In function 'anchors_getline': anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro order.c: In function 'readfile': order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'readseq': utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_arm64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_arm64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/555636 and its subdirectories I: Current time: Thu Nov 21 10:02:35 -12 2024 I: pbuilder-time-stamp: 1732226555 Thu Nov 21 22:02:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Thu Nov 21 22:02:37 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Thu Nov 21 22:02:37 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Thu Nov 21 22:02:37 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-lkFgpr' ==================================================================================== Thu Nov 21 22:02:39 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "2 lagan trixie /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY 2.0-10" as arguments. Thu Nov 21 22:02:39 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-20IHJg8F" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:02:39 UTC 2024 I: Downloading source for trixie/lagan=2.0-10 Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (9789 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (9789 kB/s) Download complete and in download only mode ============================================================================= Re-Building lagan in trixie on arm64 on codethink02-arm64 now. Date: Thu Nov 21 22:02:39 GMT 2024 Date UTC: Thu Nov 21 22:02:39 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/pbuilderrc_hIHh + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' lagan = debian-installer -o lagan = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' lagan = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.oFarX4CY/pbuilderrc_hIHh --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.oFarX4CY/b2 --logfile b2/build.log lagan_2.0-10.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 12:02:39 +14 2024 I: pbuilder-time-stamp: 1732226559 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 [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1772909/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-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 Nov 21 22:02 /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/1772909/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1772909/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=6b41d1e946ad4d3c8f8c7e5ce6ea32d6 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=1772909 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.oFarX4CY/pbuilderrc_hIHh --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.oFarX4CY/b2 --logfile b2/build.log lagan_2.0-10.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 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1772909/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), libboost-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 ... 20087 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{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} 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 30.0 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Fetched 30.0 MB in 0s (132 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 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. 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Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... 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 libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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/1772909/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1772909/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/lagan-2.0/ && 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 > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.c: In function 'anchors_getline': anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readfile': order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro skiplist.c: In function 'printSLE': utils/rc.c: In function 'main': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'readseq': utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_arm64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_arm64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_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/1772909/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1772909/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/1772909 and its subdirectories I: Current time: Fri Nov 22 12:03:16 +14 2024 I: pbuilder-time-stamp: 1732226596 + false + set +x Thu Nov 21 22:03:16 UTC 2024 I: Signing ./b2/lagan_2.0-10_arm64.buildinfo as lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:03:17 UTC 2024 I: Signed ./b2/lagan_2.0-10_arm64.buildinfo as ./b2/lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:03:17 UTC 2024 - build #2 for lagan/trixie/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 22:03:17 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-20IHJg8F, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:03 b2 -rw-r--r-- 1 jenkins jenkins 1354 Mar 25 2024 lagan_2.0-10.dsc -rw------- 1 jenkins jenkins 54442 Nov 21 22:02 rbuildlog.2SZKOWb /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1: total 1108 -rw-r--r-- 1 jenkins jenkins 51700 Nov 21 22:02 build.log -rw-r--r-- 1 jenkins jenkins 846460 Nov 21 22:02 lagan-dbgsym_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 10268 Nov 21 22:02 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Nov 21 22:02 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4977 Nov 21 22:02 lagan_2.0-10_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5859 Nov 21 22:02 lagan_2.0-10_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Nov 21 22:02 lagan_2.0-10_arm64.changes -rw-r--r-- 1 jenkins jenkins 177036 Nov 21 22:02 lagan_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 1225 Nov 21 22:02 lagan_2.0-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b2: total 1100 -rw-r--r-- 1 jenkins jenkins 53647 Nov 21 22:03 build.log -rw-r--r-- 1 jenkins jenkins 846460 Nov 21 22:03 lagan-dbgsym_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 10268 Nov 21 22:03 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Nov 21 22:03 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4973 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5855 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Nov 21 22:03 lagan_2.0-10_arm64.changes -rw-r--r-- 1 jenkins jenkins 177036 Nov 21 22:03 lagan_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 1225 Nov 21 22:03 lagan_2.0-10_source.changes Thu Nov 21 22:03:18 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Thu Nov 21 22:03:18 UTC 2024 I: lagan_2.0-10_arm64.changes: Format: 1.8 Date: Mon, 25 Mar 2024 12:32:30 +0530 Source: lagan Binary: lagan lagan-dbgsym Architecture: arm64 Version: 2.0-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: lagan - highly parametrizable pairwise global genome sequence aligner Closes: 1066580 Changes: lagan (2.0-10) unstable; urgency=medium . * Team Upload. * Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066580) Checksums-Sha1: 80e22e414e123f9f0892537812df7c74ef86887c 846460 lagan-dbgsym_2.0-10_arm64.deb 3f8b5b587706cb75c811991fda233026c3b381d7 4977 lagan_2.0-10_arm64.buildinfo 12d051fe47d90a682bc7d0ac2c5dad3390e559ca 177036 lagan_2.0-10_arm64.deb Checksums-Sha256: c851a0993b61fd8b5ba7614ec1f230a747b389e32882bdb09347df9e574686ab 846460 lagan-dbgsym_2.0-10_arm64.deb edf0f0979817c517ae3a8e2ed6726e762460b8e79a3aa379a1b0b1c9f62f98fb 4977 lagan_2.0-10_arm64.buildinfo 8ddc81abf8c41d0f69367be3ea6471ef65c75bfa2d5e683cba8a7b588cb9006e 177036 lagan_2.0-10_arm64.deb Files: 55bbb60faf0ffcf99728697d15ecca7c 846460 debug optional lagan-dbgsym_2.0-10_arm64.deb 247a9205a38639abfafdcc7f2083f6db 4977 science optional lagan_2.0-10_arm64.buildinfo 382fae398f1e0f60edf242eeb0cfaf9d 177036 science optional lagan_2.0-10_arm64.deb 113c113 < libsystemd0 (= 257~rc2-3), --- > libsystemd0 (= 256.7-3), 119c119 < libudev1 (= 257~rc2-3), --- > libudev1 (= 256.7-3), ============================================================================= Thu Nov 21 22:03:18 UTC 2024 - The installed build depends vary according to the two .buildinfo files, probably due to mirror updates. Doing the first build on codethink04-arm64.debian.net again. ============================================================================= Thu Nov 21 22:03:18 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Nov 21 22:03:18 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 22:03:18 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-bIrzLi' ==================================================================================== Thu Nov 21 22:03:20 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 lagan trixie /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY 2.0-10" as arguments. Thu Nov 21 22:03:20 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-4SUVGGx0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:03:20 UTC 2024 I: Downloading source for trixie/lagan=2.0-10 Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (11.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 205 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main lagan 2.0-10 (dsc) [1354 B] Get:2 http://deb.debian.org/debian trixie/main lagan 2.0-10 (tar) [193 kB] Get:3 http://deb.debian.org/debian trixie/main lagan 2.0-10 (diff) [10.3 kB] Fetched 205 kB in 0s (11.2 MB/s) Download complete and in download only mode ============================================================================= Building lagan in trixie on arm64 on codethink04-arm64 now. Date: Thu Nov 21 22:03:21 GMT 2024 Date UTC: Thu Nov 21 22:03:21 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 10:03:21 -12 2024 I: pbuilder-time-stamp: 1732226601 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 [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/611961/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='9f447fced6624b8f9def570f60db3ff5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='611961' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/pbuilderrc_bUZ2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/611961/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), libboost-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 ... 20087 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{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} 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 30.0 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Fetched 30.0 MB in 0s (176 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 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_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_arm64.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) ... 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-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 .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/lagan-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readfile': utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ anchors.c: In function 'anchors_getline': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': utils/scorecontigs.c: In function 'readseq': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_arm64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_arm64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/611961 and its subdirectories I: Current time: Thu Nov 21 10:03:53 -12 2024 I: pbuilder-time-stamp: 1732226633 Thu Nov 21 22:03:53 UTC 2024 I: Signing ./b1/lagan_2.0-10_arm64.buildinfo as lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:03:53 UTC 2024 I: Signed ./b1/lagan_2.0-10_arm64.buildinfo as ./b1/lagan_2.0-10_arm64.buildinfo.asc Thu Nov 21 22:03:53 UTC 2024 - build #1 for lagan/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 22:03:53 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-4SUVGGx0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY: total 80 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:03 b2 -rw-r--r-- 1 jenkins jenkins 1354 Mar 25 2024 lagan_2.0-10.dsc -rw------- 1 jenkins jenkins 56059 Nov 21 22:03 rbuildlog.2SZKOWb -rw------- 1 jenkins jenkins 3931 Nov 21 22:03 tmp.Q43HvFxch7 -rw------- 1 jenkins jenkins 3927 Nov 21 22:03 tmp.Sjc0q1EX3c /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1: total 1108 -rw-r--r-- 1 jenkins jenkins 51700 Nov 21 22:03 build.log -rw-r--r-- 1 jenkins jenkins 846460 Nov 21 22:03 lagan-dbgsym_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 10268 Nov 21 22:03 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Nov 21 22:03 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4977 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5859 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Nov 21 22:03 lagan_2.0-10_arm64.changes -rw-r--r-- 1 jenkins jenkins 177036 Nov 21 22:03 lagan_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 1225 Nov 21 22:03 lagan_2.0-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b2: total 1112 -rw-r--r-- 1 jenkins jenkins 53647 Nov 21 22:03 build.log -rw-r--r-- 1 jenkins jenkins 846460 Nov 21 22:03 lagan-dbgsym_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 10268 Nov 21 22:03 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Nov 21 22:03 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4973 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5855 Nov 21 22:03 lagan_2.0-10_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Nov 21 22:03 lagan_2.0-10_arm64.changes -rw-r--r-- 1 jenkins jenkins 177036 Nov 21 22:03 lagan_2.0-10_arm64.deb -rw-r--r-- 1 jenkins jenkins 1225 Nov 21 22:03 lagan_2.0-10_source.changes Thu Nov 21 22:03:54 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 10:03:21 -12 2024 I: pbuilder-time-stamp: 1732226601 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 [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/611961/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='9f447fced6624b8f9def570f60db3ff5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='611961' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/pbuilderrc_bUZ2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/611961/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), libboost-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 ... 20087 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{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} 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 30.0 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-3.2 [10.6 MB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Fetched 30.0 MB in 0s (176 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 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_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_arm64.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 libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-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 .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../29-libboost1.83-dev_1.83.0-3.2_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../30-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libboost1.83-dev:arm64 (1.83.0-3.2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... 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 libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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: Running cd /build/reproducible-path/lagan-2.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readfile': utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ anchors.c: In function 'anchors_getline': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': utils/scorecontigs.c: In function 'readseq': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_arm64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_arm64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/611961 and its subdirectories I: Current time: Thu Nov 21 10:03:53 -12 2024 I: pbuilder-time-stamp: 1732226633 113c113 < libsystemd0 (= 257~rc2-3), --- > libsystemd0 (= 256.7-3), 119c119 < libudev1 (= 257~rc2-3), --- > libudev1 (= 256.7-3), UPDATE 1 Thu Nov 21 22:03:55 UTC 2024 - https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/45493/console.log encountered a problem: different packages were installed in the 1st+2nd builds and also in the 2nd+3rd build. -rw-r--r-- 1 jenkins jenkins 4977 Nov 21 22:03 ./b1/lagan_2.0-10_arm64.buildinfo on codethink04-arm64.debian.net -rw-r--r-- 1 jenkins jenkins 4973 Nov 21 22:03 ./b2/lagan_2.0-10_arm64.buildinfo on codethink02-arm64.debian.net Starting cleanup. /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/rbuildlog.2SZKOWb: 83.1% -- replaced with /srv/reproducible-results/rbuild-debian/r-b-build.oFarX4CY/rbuildlog.2SZKOWb.gz [2024-11-21 22:03:55] INFO: Starting at 2024-11-21 22:03:55.655379 [2024-11-21 22:03:55] INFO: Generating the pages of 1 package(s) [2024-11-21 22:03:56] INFO: Finished at 2024-11-21 22:03:56.124853, took: 0:00:00.469482 All cleanup done. Thu Nov 21 22:03:56 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-KkOtZ8Kh, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 4.303s CPU time consumed: 5.871s