Running as unit: rb-build-amd64_23-47685.service ==================================================================================== Sat Feb 22 09:19:39 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_23) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Sat Feb 22 09:19:39 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-PJYtA1aI" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 09:19:39 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Sat Feb 22 09:19:39 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-0Zz0KU' Sat Feb 22 09:19:39 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sat Feb 22 09:19:39 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-sf2ChI' 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 amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Sat Feb 22 09:19:46 UTC 2025 I: starting to build lagan/trixie/amd64 on jenkins on '2025-02-22 09:19' Sat Feb 22 09:19:46 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/47685/console.log 1740215986 amd64 trixie lagan Sat Feb 22 09:19:46 UTC 2025 I: Downloading source for trixie/lagan=2.0-10 --2025-02-22 09:19:46-- 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% 245M=0s 2025-02-22 09:19:46 (245 MB/s) - ‘lagan_2.0-10.dsc’ saved [1354/1354] --2025-02-22 09:19:46-- 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% 245M=0s 2025-02-22 09:19:46 (245 MB/s) - ‘lagan_2.0-10.dsc’ saved [1354/1354] Sat Feb 22 09:19:46 UTC 2025 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----- Sat Feb 22 09:19:46 UTC 2025 I: Checking whether the package is not for us Sat Feb 22 09:19:46 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sat Feb 22 09:19:46 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sat Feb 22 09:19:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Sat Feb 22 09:19:46 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-aZ8VmS' ==================================================================================== Sat Feb 22 09:19:47 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 lagan trixie /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R 2.0-10" as arguments. Sat Feb 22 09:19:47 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-ocCQI6PW" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 09:19:47 UTC 2025 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 (2412 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 (2412 kB/s) Download complete and in download only mode ============================================================================= Building lagan in trixie on amd64 on ionos11-amd64 now. Date: Sat Feb 22 09:19:48 UTC 2025 Date UTC: Sat Feb 22 09:19:48 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 21:19:49 -12 2025 I: pbuilder-time-stamp: 1740215989 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 dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: unsupported subcommand 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/2287016/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b237b2d291d94d3aa10437958520eca9' 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='2287016' 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.07q5SM2R/pbuilderrc_6cQ0 --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.07q5SM2R/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2287016/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19858 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 31.2 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Fetched 31.2 MB in 8s (4040 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libboost1.83-dev:amd64. Preparing to unpack .../30-libboost1.83-dev_1.83.0-4.1_amd64.deb ... Unpacking libboost1.83-dev:amd64 (1.83.0-4.1) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_amd64.deb ... Unpacking libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libboost1.83-dev:amd64 (1.83.0-4.1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... 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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 amd64 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 -j20 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 -j20 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -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])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': 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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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/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/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/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/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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~ 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/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/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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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++ 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 -j20 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 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-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-deb: building package 'lagan' in '../lagan_2.0-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2287016 and its subdirectories I: Current time: Fri Feb 21 21:23:11 -12 2025 I: pbuilder-time-stamp: 1740216191 Sat Feb 22 09:23:11 UTC 2025 I: Signing ./b1/lagan_2.0-10_amd64.buildinfo as lagan_2.0-10_amd64.buildinfo.asc Sat Feb 22 09:23:11 UTC 2025 I: Signed ./b1/lagan_2.0-10_amd64.buildinfo as ./b1/lagan_2.0-10_amd64.buildinfo.asc Sat Feb 22 09:23:11 UTC 2025 - build #1 for lagan/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Sat Feb 22 09:23:11 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ocCQI6PW, removing. /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 09:23 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 09:19 b2 -rw-r--r-- 1 jenkins jenkins 1354 Mar 25 2024 lagan_2.0-10.dsc -rw------- 1 jenkins jenkins 2433 Feb 22 09:19 rbuildlog.6KhUWcc /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b1: total 1112 -rw-r--r-- 1 jenkins jenkins 51179 Feb 22 09:23 build.log -rw-r--r-- 1 jenkins jenkins 854744 Feb 22 09:23 lagan-dbgsym_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 10268 Feb 22 09:23 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Feb 22 09:23 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4897 Feb 22 09:23 lagan_2.0-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5779 Feb 22 09:23 lagan_2.0-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Feb 22 09:23 lagan_2.0-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 184860 Feb 22 09:23 lagan_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1225 Feb 22 09:23 lagan_2.0-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b2: total 0 Sat Feb 22 09:23:12 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 21:19:49 -12 2025 I: pbuilder-time-stamp: 1740215989 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 dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: unsupported subcommand 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/2287016/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b237b2d291d94d3aa10437958520eca9' 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='2287016' 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.07q5SM2R/pbuilderrc_6cQ0 --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.07q5SM2R/b1 --logfile b1/build.log lagan_2.0-10.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2287016/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19858 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 31.2 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Fetched 31.2 MB in 8s (4040 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libboost1.83-dev:amd64. Preparing to unpack .../30-libboost1.83-dev_1.83.0-4.1_amd64.deb ... Unpacking libboost1.83-dev:amd64 (1.83.0-4.1) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_amd64.deb ... Unpacking libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libboost1.83-dev:amd64 (1.83.0-4.1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... 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 amd64 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 -j20 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 -j20 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -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])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': 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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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/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/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/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/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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~ 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/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/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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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++ 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 -j20 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 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-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-deb: building package 'lagan' in '../lagan_2.0-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2287016 and its subdirectories I: Current time: Fri Feb 21 21:23:11 -12 2025 I: pbuilder-time-stamp: 1740216191 Sat Feb 22 09:23:13 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sat Feb 22 09:23:13 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sat Feb 22 09:23:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sat Feb 22 09:23:13 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-9aKrOE' ==================================================================================== Fri Mar 27 15:46:13 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 lagan trixie /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R 2.0-10" as arguments. Fri Mar 27 15:46:13 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-gxFvbPSo" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 15:46:13 UTC 2026 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 (2233 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 (2233 kB/s) Download complete and in download only mode ============================================================================= Re-Building lagan in trixie on amd64 on ionos15-amd64 now. Date: Fri Mar 27 15:46:14 UTC 2026 Date UTC: Fri Mar 27 15:46:14 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/pbuilderrc_vmPg + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${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.07q5SM2R/pbuilderrc_vmPg --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.07q5SM2R/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: Sat Mar 28 05:46:14 +14 2026 I: pbuilder-time-stamp: 1774626374 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 dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: unsupported subcommand 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/2008737/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 27 15:46 /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/2008737/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=1e582c3a978b4ca89e5e3ef8b443b90d LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2008737 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.07q5SM2R/pbuilderrc_vmPg --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.07q5SM2R/b2 --logfile b2/build.log lagan_2.0-10.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 19858 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 31.2 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Fetched 31.2 MB in 0s (87.9 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2008737/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 amd64 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 -j42 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 -j42 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -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++ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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 'readfile': utils/contigorder.c: In function 'getFileInfo': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ 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])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~ 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/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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -j42 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 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_amd64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2008737/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/2008737 and its subdirectories I: Current time: Sat Mar 28 05:48:33 +14 2026 I: pbuilder-time-stamp: 1774626513 + false + set +x Fri Mar 27 15:48:33 UTC 2026 I: Signing ./b2/lagan_2.0-10_amd64.buildinfo as lagan_2.0-10_amd64.buildinfo.asc Fri Mar 27 15:48:33 UTC 2026 I: Signed ./b2/lagan_2.0-10_amd64.buildinfo as ./b2/lagan_2.0-10_amd64.buildinfo.asc Fri Mar 27 15:48:33 UTC 2026 - build #2 for lagan/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Fri Mar 27 15:48:33 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-gxFvbPSo, removing. /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 09:23 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 09:25 b2 -rw-r--r-- 1 jenkins jenkins 1354 Mar 25 2024 lagan_2.0-10.dsc -rw------- 1 jenkins jenkins 53901 Feb 22 09:23 rbuildlog.6KhUWcc /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b1: total 1124 -rw-r--r-- 1 jenkins jenkins 51179 Feb 22 09:23 build.log -rw-r--r-- 1 jenkins jenkins 854744 Feb 22 09:23 lagan-dbgsym_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 10268 Feb 22 09:23 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Feb 22 09:23 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4897 Feb 22 09:23 lagan_2.0-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5779 Feb 22 09:23 lagan_2.0-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Feb 22 09:23 lagan_2.0-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 184860 Feb 22 09:23 lagan_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1225 Feb 22 09:23 lagan_2.0-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b2: total 1112 -rw-r--r-- 1 jenkins jenkins 53120 Feb 22 09:25 build.log -rw-r--r-- 1 jenkins jenkins 854744 Feb 22 09:25 lagan-dbgsym_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 10268 Feb 22 09:25 lagan_2.0-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1354 Feb 22 09:25 lagan_2.0-10.dsc -rw-r--r-- 1 jenkins jenkins 4906 Feb 22 09:25 lagan_2.0-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5788 Feb 22 09:25 lagan_2.0-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1374 Feb 22 09:25 lagan_2.0-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 184860 Feb 22 09:25 lagan_2.0-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1225 Feb 22 09:25 lagan_2.0-10_source.changes Sat Feb 22 09:25:34 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sat Feb 22 09:25:34 UTC 2025 I: lagan_2.0-10_amd64.changes: Format: 1.8 Date: Mon, 25 Mar 2024 12:32:30 +0530 Source: lagan Binary: lagan lagan-dbgsym Architecture: amd64 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: 5cb4f1dab75fd678496e84d4bc78bc878420790e 854744 lagan-dbgsym_2.0-10_amd64.deb 54ecc78ccfa627a8b6bfce701e787f731638c528 4897 lagan_2.0-10_amd64.buildinfo 7aa8f79a12ca7638411024d252c71324dcfe8507 184860 lagan_2.0-10_amd64.deb Checksums-Sha256: 579e83cf01e8e28af53f6822877bc9917c8df9cf53099a9d335ce172440484fb 854744 lagan-dbgsym_2.0-10_amd64.deb 2e15bfc1c3edabc9253a6d108044de1cf87abdd5f1f849bd8473ba99f15b3955 4897 lagan_2.0-10_amd64.buildinfo 51e6a782bd89e0435d3bdd34cab51f25cb8ed2da8fef44eef06fd9e3375f5bb5 184860 lagan_2.0-10_amd64.deb Files: 35723c9a7f0dbed08440477dceb3ede2 854744 debug optional lagan-dbgsym_2.0-10_amd64.deb 11fa191e2e5d43da1a90f1045ec39681 4897 science optional lagan_2.0-10_amd64.buildinfo 4c34e2a1b0287d59c07885bc2fa929a1 184860 science optional lagan_2.0-10_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/lagan_2.0-10.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/lagan_2.0-10.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/lagan_2.0-10.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/lagan_2.0-10.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/lagan_2.0-10_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/lagan_2.0-10.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 09:23:12.486119127 +0000 +++ b2/build.log 2025-02-22 09:25:34.019751456 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 21 21:19:49 -12 2025 -I: pbuilder-time-stamp: 1740215989 +I: Current time: Sat Mar 28 05:46:14 +14 2026 +I: pbuilder-time-stamp: 1774626374 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ 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/2287016/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 27 15:46 /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/2008737/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2008737/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b237b2d291d94d3aa10437958520eca9' - 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='2287016' - PS1='# ' - PS2='> ' + INVOCATION_ID=1e582c3a978b4ca89e5e3ef8b443b90d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2008737 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.07q5SM2R/pbuilderrc_6cQ0 --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.07q5SM2R/b1 --logfile b1/build.log lagan_2.0-10.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.07q5SM2R/pbuilderrc_vmPg --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.07q5SM2R/b2 --logfile b2/build.log lagan_2.0-10.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2287016/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -149,7 +181,7 @@ Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] -Fetched 31.2 MB in 8s (4040 kB/s) +Fetched 31.2 MB in 0s (87.9 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) @@ -292,7 +324,11 @@ 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 +I: user script /srv/workspace/pbuilder/2008737/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2008737/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 @@ -304,7 +340,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean - make -j20 clean + make -j42 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 @@ -327,7 +363,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src - cd src && make -j20 "INSTALL=install --strip-program=true" + cd src && make -j42 "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 -fcf-protection -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 -fcf-protection -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 @@ -340,31 +376,56 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -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++ +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/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +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/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); + | ^~~~~~~~~~~~~~~~~~~~~~~ +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 'readfile': utils/contigorder.c: In function 'getFileInfo': +fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] + 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ @@ -376,12 +437,27 @@ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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); + | ^~~~~~~~~~~~~~~~~~~~~~~ +mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 81 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -402,48 +478,31 @@ 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])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c: In function 'readfile': -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] - 357 | 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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ -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/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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 81 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ +utils/scorecontigs.c: In function 'main': fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ +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/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -453,26 +512,6 @@ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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/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/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); @@ -486,39 +525,40 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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/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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -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 -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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/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); @@ -536,10 +576,6 @@ | | | | unsigned int void * | %p -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/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"; @@ -656,14 +692,14 @@ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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 -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fcf-protection -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); @@ -673,7 +709,7 @@ 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 -j20 test + make -j42 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' @@ -714,8 +750,8 @@ dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-deb: building package 'lagan' in '../lagan_2.0-10_amd64.deb'. +dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -723,12 +759,14 @@ 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/2008737/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2008737/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/2287016 and its subdirectories -I: Current time: Fri Feb 21 21:23:11 -12 2025 -I: pbuilder-time-stamp: 1740216191 +I: removing directory /srv/workspace/pbuilder/2008737 and its subdirectories +I: Current time: Sat Mar 28 05:48:33 +14 2026 +I: pbuilder-time-stamp: 1774626513 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/lagan_2.0-10.diff: 83.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/lagan_2.0-10.diff.gz b2/build.log: 83.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.8% -- replaced with stdout Sat Feb 22 09:25:35 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_lagan_trixie_amd64_1740216335 + touch /var/log/reproducible-builds/diffoscope_stamp_lagan_trixie_amd64_1740216335 + RESULT=0 + systemd-run '--description=diffoscope on lagan/2.0-10 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_23-47685 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R --run-session -c jenkins-reproducible-trixie-diffoscope-138e83ff-b48e-4a55-9d6e-9b40ffcb2647 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/dbd-tmp-giUDjd3 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b1/lagan_2.0-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b2/lagan_2.0-10_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_23-47685.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/lagan_2.0-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b1/lagan_2.0-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.07q5SM2R/b2/lagan_2.0-10_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 258ms CPU time consumed: 253ms _ | | __ _ __ _ __ _ _ __ | |/ _` |/ _` |/ _` | '_ \ | | (_| | (_| | (_| | | | | |_|\__,_|\__, |\__,_|_| |_| |___/ Sat Feb 22 09:25:36 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sat Feb 22 09:25:36 UTC 2025 I: lagan from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-22 09:25:36] INFO: Starting at 2025-02-22 09:25:36.685736 [2025-02-22 09:25:36] INFO: Generating the pages of 1 package(s) [2025-02-22 09:25:36] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/lagan didn't produce a buildlog, even though it has been built. [2025-02-22 09:25:37] INFO: Finished at 2025-02-22 09:25:37.072332, took: 0:00:00.386604 Sat Feb 22 09:25:37 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/lagan.html Sat Feb 22 09:25:37 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Feb 22 09:25:37 UTC 2025 I: Submitting 8.0K b1/lagan_2.0-10_amd64.buildinfo.asc https://buildinfo.debian.net/54ecc78ccfa627a8b6bfce701e787f731638c528/lagan_2.0-10_amd64 Sat Feb 22 09:25:38 UTC 2025 I: Submitting 8.0K b2/lagan_2.0-10_amd64.buildinfo.asc https://buildinfo.debian.net/b6b94946e01c22dfb803e81958a5185f79e4b5d6/lagan_2.0-10_amd64 Sat Feb 22 09:25:38 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Feb 22 09:25:38 UTC 2025 I: Done submitting .buildinfo files. Sat Feb 22 09:25:38 UTC 2025 I: Removing signed lagan_2.0-10_amd64.buildinfo.asc files: removed './b1/lagan_2.0-10_amd64.buildinfo.asc' removed './b2/lagan_2.0-10_amd64.buildinfo.asc' 1740216338 amd64 trixie lagan Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/lagan_2.0-10.rbuild.log: 81.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/lagan_2.0-10.rbuild.log.gz [2025-02-22 09:25:39] INFO: Starting at 2025-02-22 09:25:39.376056 [2025-02-22 09:25:39] INFO: Generating the pages of 1 package(s) [2025-02-22 09:25:40] INFO: Finished at 2025-02-22 09:25:40.286990, took: 0:00:00.910947 All cleanup done. Sat Feb 22 09:25:40 UTC 2025 - total duration: 0h 5m 57s. Sat Feb 22 09:25:40 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-PJYtA1aI, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 1.226s CPU time consumed: 7.663s