Running as unit: rb-build-amd64_22-29926.service ==================================================================================== Tue Jan 7 21:51:39 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_22) on jenkins, called using "ionos5-amd64 ionos11-amd64" as arguments. Tue Jan 7 21:51:39 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-oZxOVGvl" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 7 21:51:39 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Jan 7 21:51:39 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-GFFpJF' Tue Jan 7 21:51:40 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Jan 7 21:51:40 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-3usFpT' ok, let's check if spaln is building anywhere yet… ok, spaln is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of spaln in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Tue Jan 7 21:52:02 UTC 2025 I: starting to build spaln/unstable/amd64 on jenkins on '2025-01-07 21:51' Tue Jan 7 21:52:02 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/29926/console.log 1736286722 amd64 unstable spaln Tue Jan 7 21:52:02 UTC 2025 I: Downloading source for unstable/spaln=3.0.2+dfsg-2 --2025-01-07 21:52:02-- http://deb.debian.org/debian/pool/main/s/spaln/spaln_3.0.2%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2224 (2.2K) [text/prs.lines.tag] Saving to: ‘spaln_3.0.2+dfsg-2.dsc’ 0K .. 100% 287M=0s 2025-01-07 21:52:02 (287 MB/s) - ‘spaln_3.0.2+dfsg-2.dsc’ saved [2224/2224] --2025-01-07 21:52:02-- http://deb.debian.org/debian/pool/main/s/spaln/spaln_3.0.2%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2224 (2.2K) [text/prs.lines.tag] Saving to: ‘spaln_3.0.2+dfsg-2.dsc’ 0K .. 100% 287M=0s 2025-01-07 21:52:02 (287 MB/s) - ‘spaln_3.0.2+dfsg-2.dsc’ saved [2224/2224] Tue Jan 7 21:52:02 UTC 2025 I: spaln_3.0.2+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: spaln Binary: spaln, spaln-data Architecture: amd64 arm64 loong64 mips64el ppc64el s390x alpha ia64 kfreebsd-amd64 ppc64 riscv64 sparc64 all Version: 3.0.2+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/ogotoh/spaln Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/spaln Vcs-Git: https://salsa.debian.org/med-team/spaln.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libgsl-dev Package-List: spaln deb science optional arch=amd64,arm64,loong64,mips64el,ppc64el,s390x,alpha,ia64,kfreebsd-amd64,ppc64,riscv64,sparc64 spaln-data deb science optional arch=all Checksums-Sha1: 6d71b8bb7e3a9c69dd4142c5f9ac42a26982bb00 19782380 spaln_3.0.2+dfsg.orig.tar.xz d2836b50c01cc39750a9728877f740d375ee7b65 6124 spaln_3.0.2+dfsg-2.debian.tar.xz Checksums-Sha256: 323d16a645b8c1194a81e20aa073482dd2d9099cd7d07c521cab452261d81166 19782380 spaln_3.0.2+dfsg.orig.tar.xz 1ad652d39ebf50ceba8b6ab1c4e475357d4dec95114c36a8a3df37e2252f31fb 6124 spaln_3.0.2+dfsg-2.debian.tar.xz Files: b2f03433bc27b3f6cc5d12b8341a18ea 19782380 spaln_3.0.2+dfsg.orig.tar.xz df0fcd7e2c199d7dc6375d502426f393 6124 spaln_3.0.2+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmXKg9URHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF6nA/9GuszpJ58JHsvNF59ncvqMb8IUMBjUFzA RGhc3peRb2EAXJ2UiM+1aEenQ5yVOWhJJAIoEFpKUH1v++lven+KVAN46iuTu5Ri N71JcY4munWRgf0Wrii80a4tBVKLKO6gUD4zxNYypOPPSfalwu8Mra0tiCowQwgU zoznjUJGdbFDd9vGVUmhqeEnCkSrxaeg1CKN0eNXtlwxe8YYV6KdunJa8SsqioWO bMEOSecPnPpr/giJWVhOkCgDMXggczADczOw69P5EbXpEfTnz/bKkm+5oy509NHr AhQ0bCfLFNAG5iu7WY40JlYI2o9RkRVF6BcCBrPVVg67d02mZoUkyXPA9abFsk8S 7EdkE0B2SNUT4CWv6XhaY4Do+iEoZ2eWEVpufbE2COB7bfxWfc46y2S3beY56xQL AOXPLGb42Japytn/IJCmCaOI3mnmLIqRJuQlanMPNqDFdbQY6s1mqLULPelUivZR APRo+yet/gYYo+2u4UREmNvBCIb9Mg/urczAYbBelivQD/gvhIl5zD0N6J5iQ+xV tCkELRVg3r6l2JAwPwjMPVRw4K4IwzwHsSjK0S08MWg3thff1ELC3KO8ojEijDGT GqMNji3ors1+E+wkTj2xpfz0+L/gZBZK3e0r/w6jXYLw5KsFKx2MCS/yX61Ii4H7 QvUbknNnOrQ= =fdQG -----END PGP SIGNATURE----- Tue Jan 7 21:52:02 UTC 2025 I: Checking whether the package is not for us Tue Jan 7 21:52:02 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Jan 7 21:52:02 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Jan 7 21:52:02 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Jan 7 21:52:02 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ZYgQou' ==================================================================================== Tue Feb 10 04:15:03 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 spaln unstable /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX 3.0.2+dfsg-2" as arguments. Tue Feb 10 04:15:03 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-gXB74jvX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Feb 10 04:15:03 UTC 2026 I: Downloading source for unstable/spaln=3.0.2+dfsg-2 Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (77.7 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (77.7 MB/s) Download complete and in download only mode ============================================================================= Building spaln in unstable on amd64 on ionos5-amd64 now. Date: Tue Feb 10 04:15:04 UTC 2026 Date UTC: Tue Feb 10 04:15:04 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 9 16:15:04 -12 2026 I: pbuilder-time-stamp: 1770696904 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spaln_3.0.2+dfsg-2.dsc] I: copying [./spaln_3.0.2+dfsg.orig.tar.xz] I: copying [./spaln_3.0.2+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spaln_3.0.2+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting spaln in spaln-3.0.2+dfsg dpkg-source: info: unpacking spaln_3.0.2+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_3.0.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying add_path_to_testscript.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3405471/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='dae41a8558fe4c2fa2100e3b848501d2' 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='3405471' 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.9qh6YiaX/pbuilderrc_8G9w --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1 --logfile b1/build.log spaln_3.0.2+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3405471/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), zlib1g-dev, libgsl-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 ... 19848 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 90.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-13 [91.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 23.6 MB in 2s (9861 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 ... 19848 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_0.22.5-4_amd64.deb ... Unpacking gettext-base (0.22.5-4) ... 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_2.40.2-13_amd64.deb ... Unpacking bsdextrautils (2.40.2-13) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64: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_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... 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_0.22.5-4_amd64.deb ... Unpacking gettext (0.22.5-4) ... 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Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/spaln-3.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spaln_3.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 3.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/spaln.substvars debian/spaln-data.substvars debian/files rm -fr -- debian/spaln/ debian/tmp/ debian/spaln-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" exec_prefix=/usr/bin table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb ./configure OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic binaries install to /usr/bin tables install to /usr/share/spaln/table alndbs install to /usr/share/spaln/seqdb wrote Makefile wrote files OK. try make and make install. good luck! make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j42 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gaps.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c divseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gsinfo.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2d1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2h1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2s1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c bitpat.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c seq.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c simmtx.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sqpr.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utilseq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c vmf.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c wln.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c boyer_moore.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c clib.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c iolib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c mfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sets.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c supprime.cc 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++ 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++ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:483:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 483 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 484 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* x86_64-linux-gnu-ar rc clib.a clib.o iolib.o mfile.o sets.o supprime.o x86_64-linux-gnu-ranlib clib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc sblib.a aln2.o dbs.o gaps.o codepot.o divseq.o gsinfo.o \ fwd2b1.o fwd2d1.o fwd2h1.o fwd2s1.o bitpat.o eijunc.o \ seq.o simmtx.o sqpr.o utilseq.o vmf.o wln.o boyer_moore.o x86_64-linux-gnu-ranlib sblib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o spaln spaln.cc blksrc.o sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o sortgrcd sortgrcd.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now 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++ sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:999:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 999 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.isra': spaln.cc:858:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 858 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'match_2', inlined from 'spaln_job' at spaln.cc:1142:14: spaln.cc:764:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 764 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new: In function 'spaln_job': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c autocomp.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c extcds.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c montseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c pattern.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c resite.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o exinpot exinpot.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o kmers kmers.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o npssm npssm.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utn.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c ildpdf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c decompild.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fitild.cc 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++ 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++ 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++ x86_64-linux-gnu-ar rc ublib.a autocomp.o extcds.o \ montseq.o pattern.o resite.o x86_64-linux-gnu-ranlib ublib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o dvn dvn.cc ublib.a sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o rdn rdn.cc ublib.a sblib.a clib.a -lpthread -lm -lz 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o fitild -DMAIN fitild.cc ildpdf.o clib.a -lpthread -lm -lz \ -L/usr/local/lib -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o compild compild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o decompild decompild.o ildpdf.o fitild.o clib.a -lpthread -lm -lz -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o plotild plotild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas 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++ plotild.cc: In function 'getiprms': plotild.cc:136:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 136 | IldPrm* ipprm = new IldPrm[nn + nprm + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o utn utn.o ublib.a sblib.a clib.a -lpthread -lm -lz please make install before test make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-PsILVNJa create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src rm -f -- debian/spaln.substvars debian/spaln-data.substvars rm -fr -- debian/.debhelper/generated/spaln/ debian/spaln/ debian/tmp/ debian/.debhelper/generated/spaln-data/ debian/spaln-data/ rm -f debian/spaln-data.debhelper.log debian/spaln.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_install -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin install -m0755 -d /build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp cd src && make -j42 install DESTDIR=/build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin if [ -s spaln ]; then\ cp spaln sortgrcd makmdm makdbs /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s exinpot ]; then \ cp dvn exinpot kmers npssm rdn utn /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s fitild ]; then \ cp fitild compild decompild plotild /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table ./makmdm /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table 7.6862 5.1057 4.2546 5.1269 2.0279 4.1061 6.1820 7.4714 2.2983 5.2569 9.1111 5.9498 2.3414 4.0530 5.0532 6.8225 5.8518 1.4336 3.2303 6.6374 Pam = 0 Norl fact = 106.899 trace = 106.899 Pam = 10 Norl fact = 13.996 trace = 41.995 Pam = 20 Norl fact = 15.588 trace = 45.299 Pam = 30 Norl fact = 16.894 trace = 47.531 Pam = 40 Norl fact = 18.094 trace = 49.266 Pam = 50 Norl fact = 19.249 trace = 50.701 Pam = 60 Norl fact = 20.386 trace = 51.928 Pam = 70 Norl fact = 21.522 trace = 52.997 Pam = 80 Norl fact = 22.667 trace = 53.943 Pam = 90 Norl fact = 23.828 trace = 54.788 Pam = 100 Norl fact = 25.012 trace = 55.547 Pam = 110 Norl fact = 26.222 trace = 56.234 Pam = 120 Norl fact = 27.462 trace = 56.858 Pam = 130 Norl fact = 28.735 trace = 57.427 Pam = 140 Norl fact = 30.044 trace = 57.946 Pam = 150 Norl fact = 31.391 trace = 58.421 Pam = 160 Norl fact = 32.778 trace = 58.858 Pam = 170 Norl fact = 34.208 trace = 59.259 Pam = 180 Norl fact = 35.683 trace = 59.629 Pam = 190 Norl fact = 37.204 trace = 59.970 Pam = 200 Norl fact = 38.774 trace = 60.286 Pam = 210 Norl fact = 40.394 trace = 60.580 Pam = 220 Norl fact = 42.066 trace = 60.854 Pam = 230 Norl fact = 43.793 trace = 61.110 Pam = 240 Norl fact = 45.577 trace = 61.350 Pam = 250 Norl fact = 47.419 trace = 61.576 Pam = 260 Norl fact = 49.322 trace = 61.791 Pam = 270 Norl fact = 51.287 trace = 61.996 Pam = 280 Norl fact = 53.318 trace = 62.191 Pam = 290 Norl fact = 55.415 trace = 62.380 Pam = 300 Norl fact = 57.582 trace = 62.563 test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_install -O--sourcedirectory=src install -m0755 -d debian/spaln//usr cp --reflink=auto -a debian/tmp/usr/bin debian/spaln//usr/ install -m0755 -d debian/spaln-data//usr cp --reflink=auto -a debian/tmp/usr/share debian/spaln-data//usr/ dh_installdocs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -m0755 -d debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./README.md debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/README.test debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/tests/run-unit-test debian/spaln/usr/share/doc/spaln chmod -R u\+rw,go=rX debian/spaln/usr/share/doc install -p -m0644 debian/README.Debian debian/spaln/usr/share/doc/spaln/README.Debian install -p -m0644 debian/copyright debian/spaln/usr/share/doc/spaln/copyright install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/copyright debian/spaln-data/usr/share/doc/spaln-data/copyright dh_installchangelogs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -p -m0644 debian/.debhelper/generated/spaln/dh_installchangelogs.dch.trimmed debian/spaln/usr/share/doc/spaln/changelog.Debian install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/.debhelper/generated/spaln-data/dh_installchangelogs.dch.trimmed debian/spaln-data/usr/share/doc/spaln-data/changelog.Debian dh_installman -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./sortgrcd.1 debian/spaln/usr/share/man/man1/sortgrcd.1 install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./spaln.1 debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/spaln.1.dh-new debian/spaln/usr/share/man/man1/spaln.1 chmod 0644 -- debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- debian/spaln/usr/share/man/man1/sortgrcd.1 dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src mv debian/spaln-data.substvars.new debian/spaln-data.substvars dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src Using 1707770215 as canonical time Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.faa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.cf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc_g.gf.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--sourcedirectory=src cd debian/spaln cd debian/spaln-data chmod a-x usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 chmod a-x usr/share/doc/spaln-data/changelog.Debian gzip -9nf usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 gzip -9nf usr/share/doc/spaln-data/changelog.Debian cd '/build/reproducible-path/spaln-3.0.2+dfsg' cd '/build/reproducible-path/spaln-3.0.2+dfsg' dh_fixperms -O--sourcedirectory=src find debian/spaln ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/spaln-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -- debian/spaln/usr/bin/compild debian/spaln/usr/bin/decompild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/fitild debian/spaln/usr/bin/kmers debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/npssm debian/spaln/usr/bin/plotild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln debian/spaln/usr/bin/utn objcopy --compress-debug-sections debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug chmod 0644 -- debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug dh_strip -a -O--sourcedirectory=src install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makdbs objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/kmers debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/kmers objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug debian/spaln/usr/bin/kmers install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/spaln objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/dvn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/dvn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug debian/spaln/usr/bin/dvn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/fitild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/fitild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug debian/spaln/usr/bin/fitild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/compild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/compild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug debian/spaln/usr/bin/compild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/exinpot debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/exinpot objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug debian/spaln/usr/bin/exinpot install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/utn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/utn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug debian/spaln/usr/bin/utn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/plotild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/plotild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug debian/spaln/usr/bin/plotild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makmdm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug debian/spaln/usr/bin/makmdm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/decompild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/decompild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug debian/spaln/usr/bin/decompild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/rdn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/rdn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug debian/spaln/usr/bin/rdn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/sortgrcd objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/npssm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/npssm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug debian/spaln/usr/bin/npssm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/spaln/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/spaln/usr/lib/debug install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/share/doc ln -s spaln debian/.debhelper/spaln/dbgsym-root/usr/share/doc/spaln-dbgsym install -m0755 -d debian/.debhelper/spaln dh_makeshlibs -a -O--sourcedirectory=src rm -f debian/spaln/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN dpkg-shlibdeps -Tdebian/spaln.substvars debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/kmers debian/spaln/usr/bin/spaln debian/spaln/usr/bin/dvn debian/spaln/usr/bin/fitild debian/spaln/usr/bin/compild debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/utn debian/spaln/usr/bin/plotild debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/decompild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/npssm dh_installdeb -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN dh_gencontrol -O--sourcedirectory=src install -m0755 -d debian/spaln-data/DEBIAN echo misc:Depends= >> debian/spaln-data.substvars echo misc:Pre-Depends= >> debian/spaln-data.substvars dpkg-gencontrol -pspaln-data -ldebian/changelog -Tdebian/spaln-data.substvars -cdebian/control -Pdebian/spaln-data install -m0755 -d debian/spaln/DEBIAN echo misc:Depends= >> debian/spaln.substvars echo misc:Pre-Depends= >> debian/spaln.substvars install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=070ac648f6f60726285b78e733193505dd0ac3ef 1348c45ca8995d1c30fb7c902c327329b4578b21 1ce3b7e2ae0fd8793b7e04ad05cbd62cc0493655 3450d322f0e37b119842690ac80452a5fc686a00 3c3303bdc3af07eadabde6033d11f099593bcbe3 5586fef186af78965ee257b0bcb5cc4a7fba9d17 66313a39ff6d3953891b4569bcbd17851e765868 689dcc00122bec624cd104a5450a08d5001b9e88 95b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4 9c08c35d4a3b17f4727b2956ebef81c3a87d5671 abcae5f323398b73002b9bcc0214cb0cfe30d511 ca6bbb6041eee4fbdb193cf3d029c858c673c998 e5ea39d23dc4e5fac196424f8754987784c46e51 ea32f5007eff9fb98ed92ce0436ed02987f56e74" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/control dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/spaln dpkg-gencontrol: warning: package spaln-data: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/spaln-data/DEBIAN/control chmod 0644 -- debian/spaln/DEBIAN/control dh_md5sums -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN cd debian/spaln >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/spaln-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/spaln/DEBIAN/md5sums install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN cd debian/.debhelper/spaln/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/spaln-data/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src dpkg-deb --root-owner-group --build debian/spaln .. dpkg-deb --root-owner-group --build debian/.debhelper/spaln/dbgsym-root .. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln' in '../spaln_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-dbgsym' in '../spaln-dbgsym_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_3.0.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_3.0.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_3.0.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3405471 and its subdirectories I: Current time: Mon Feb 9 16:16:38 -12 2026 I: pbuilder-time-stamp: 1770696998 Tue Feb 10 04:16:38 UTC 2026 I: Signing ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo as spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Feb 10 04:16:38 UTC 2026 I: Signed ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo as ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Feb 10 04:16:38 UTC 2026 - build #1 for spaln/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Tue Feb 10 04:16:38 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-gXB74jvX, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 21:53 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 21:52 b2 -rw------- 1 jenkins jenkins 3337 Jan 7 21:52 rbuildlog.K7fv954 -rw-r--r-- 1 jenkins jenkins 2224 Feb 12 2024 spaln_3.0.2+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1: total 23168 -rw-r--r-- 1 jenkins jenkins 68512 Jan 7 21:53 build.log -rw-r--r-- 1 jenkins jenkins 19478864 Jan 7 21:53 spaln-data_3.0.2+dfsg-2_all.deb -rw-r--r-- 1 jenkins jenkins 3553100 Jan 7 21:53 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 6124 Jan 7 21:53 spaln_3.0.2+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2224 Jan 7 21:53 spaln_3.0.2+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5397 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6279 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1771 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 580300 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1258 Jan 7 21:53 spaln_3.0.2+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b2: total 0 Tue Jan 7 21:53:39 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 9 16:15:04 -12 2026 I: pbuilder-time-stamp: 1770696904 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spaln_3.0.2+dfsg-2.dsc] I: copying [./spaln_3.0.2+dfsg.orig.tar.xz] I: copying [./spaln_3.0.2+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spaln_3.0.2+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting spaln in spaln-3.0.2+dfsg dpkg-source: info: unpacking spaln_3.0.2+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_3.0.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying add_path_to_testscript.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3405471/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='dae41a8558fe4c2fa2100e3b848501d2' 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='3405471' 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.9qh6YiaX/pbuilderrc_8G9w --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1 --logfile b1/build.log spaln_3.0.2+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3405471/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), zlib1g-dev, libgsl-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 ... 19848 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 90.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-13 [91.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 23.6 MB in 2s (9861 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 ... 19848 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_0.22.5-4_amd64.deb ... Unpacking gettext-base (0.22.5-4) ... 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_2.40.2-13_amd64.deb ... Unpacking bsdextrautils (2.40.2-13) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64: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_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... 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_0.22.5-4_amd64.deb ... Unpacking gettext (0.22.5-4) ... 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_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../30-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../31-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../33-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-4) ... 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 (0.22.5-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... 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 libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... 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 (13.23) ... Processing triggers for libc-bin (2.40-5) ... 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/spaln-3.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spaln_3.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 3.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/spaln.substvars debian/spaln-data.substvars debian/files rm -fr -- debian/spaln/ debian/tmp/ debian/spaln-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" exec_prefix=/usr/bin table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb ./configure OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic binaries install to /usr/bin tables install to /usr/share/spaln/table alndbs install to /usr/share/spaln/seqdb wrote Makefile wrote files OK. try make and make install. good luck! make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j42 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gaps.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c divseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gsinfo.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2d1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2h1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2s1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c bitpat.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c seq.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c simmtx.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sqpr.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utilseq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c vmf.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c wln.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c boyer_moore.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c clib.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c iolib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c mfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sets.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c supprime.cc 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++ 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++ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:483:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 483 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 484 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* x86_64-linux-gnu-ar rc clib.a clib.o iolib.o mfile.o sets.o supprime.o x86_64-linux-gnu-ranlib clib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc sblib.a aln2.o dbs.o gaps.o codepot.o divseq.o gsinfo.o \ fwd2b1.o fwd2d1.o fwd2h1.o fwd2s1.o bitpat.o eijunc.o \ seq.o simmtx.o sqpr.o utilseq.o vmf.o wln.o boyer_moore.o x86_64-linux-gnu-ranlib sblib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o spaln spaln.cc blksrc.o sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o sortgrcd sortgrcd.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now 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++ sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:999:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 999 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.isra': spaln.cc:858:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 858 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'match_2', inlined from 'spaln_job' at spaln.cc:1142:14: spaln.cc:764:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 764 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new: In function 'spaln_job': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c autocomp.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c extcds.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c montseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c pattern.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c resite.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o exinpot exinpot.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o kmers kmers.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o npssm npssm.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utn.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c ildpdf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c decompild.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fitild.cc 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++ 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++ 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++ x86_64-linux-gnu-ar rc ublib.a autocomp.o extcds.o \ montseq.o pattern.o resite.o x86_64-linux-gnu-ranlib ublib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o dvn dvn.cc ublib.a sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o rdn rdn.cc ublib.a sblib.a clib.a -lpthread -lm -lz 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o fitild -DMAIN fitild.cc ildpdf.o clib.a -lpthread -lm -lz \ -L/usr/local/lib -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o compild compild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o decompild decompild.o ildpdf.o fitild.o clib.a -lpthread -lm -lz -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o plotild plotild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas 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++ plotild.cc: In function 'getiprms': plotild.cc:136:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 136 | IldPrm* ipprm = new IldPrm[nn + nprm + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o utn utn.o ublib.a sblib.a clib.a -lpthread -lm -lz please make install before test make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-PsILVNJa create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src rm -f -- debian/spaln.substvars debian/spaln-data.substvars rm -fr -- debian/.debhelper/generated/spaln/ debian/spaln/ debian/tmp/ debian/.debhelper/generated/spaln-data/ debian/spaln-data/ rm -f debian/spaln-data.debhelper.log debian/spaln.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_install -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin install -m0755 -d /build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp cd src && make -j42 install DESTDIR=/build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin if [ -s spaln ]; then\ cp spaln sortgrcd makmdm makdbs /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s exinpot ]; then \ cp dvn exinpot kmers npssm rdn utn /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s fitild ]; then \ cp fitild compild decompild plotild /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table ./makmdm /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table 7.6862 5.1057 4.2546 5.1269 2.0279 4.1061 6.1820 7.4714 2.2983 5.2569 9.1111 5.9498 2.3414 4.0530 5.0532 6.8225 5.8518 1.4336 3.2303 6.6374 Pam = 0 Norl fact = 106.899 trace = 106.899 Pam = 10 Norl fact = 13.996 trace = 41.995 Pam = 20 Norl fact = 15.588 trace = 45.299 Pam = 30 Norl fact = 16.894 trace = 47.531 Pam = 40 Norl fact = 18.094 trace = 49.266 Pam = 50 Norl fact = 19.249 trace = 50.701 Pam = 60 Norl fact = 20.386 trace = 51.928 Pam = 70 Norl fact = 21.522 trace = 52.997 Pam = 80 Norl fact = 22.667 trace = 53.943 Pam = 90 Norl fact = 23.828 trace = 54.788 Pam = 100 Norl fact = 25.012 trace = 55.547 Pam = 110 Norl fact = 26.222 trace = 56.234 Pam = 120 Norl fact = 27.462 trace = 56.858 Pam = 130 Norl fact = 28.735 trace = 57.427 Pam = 140 Norl fact = 30.044 trace = 57.946 Pam = 150 Norl fact = 31.391 trace = 58.421 Pam = 160 Norl fact = 32.778 trace = 58.858 Pam = 170 Norl fact = 34.208 trace = 59.259 Pam = 180 Norl fact = 35.683 trace = 59.629 Pam = 190 Norl fact = 37.204 trace = 59.970 Pam = 200 Norl fact = 38.774 trace = 60.286 Pam = 210 Norl fact = 40.394 trace = 60.580 Pam = 220 Norl fact = 42.066 trace = 60.854 Pam = 230 Norl fact = 43.793 trace = 61.110 Pam = 240 Norl fact = 45.577 trace = 61.350 Pam = 250 Norl fact = 47.419 trace = 61.576 Pam = 260 Norl fact = 49.322 trace = 61.791 Pam = 270 Norl fact = 51.287 trace = 61.996 Pam = 280 Norl fact = 53.318 trace = 62.191 Pam = 290 Norl fact = 55.415 trace = 62.380 Pam = 300 Norl fact = 57.582 trace = 62.563 test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_install -O--sourcedirectory=src install -m0755 -d debian/spaln//usr cp --reflink=auto -a debian/tmp/usr/bin debian/spaln//usr/ install -m0755 -d debian/spaln-data//usr cp --reflink=auto -a debian/tmp/usr/share debian/spaln-data//usr/ dh_installdocs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -m0755 -d debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./README.md debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/README.test debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/tests/run-unit-test debian/spaln/usr/share/doc/spaln chmod -R u\+rw,go=rX debian/spaln/usr/share/doc install -p -m0644 debian/README.Debian debian/spaln/usr/share/doc/spaln/README.Debian install -p -m0644 debian/copyright debian/spaln/usr/share/doc/spaln/copyright install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/copyright debian/spaln-data/usr/share/doc/spaln-data/copyright dh_installchangelogs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -p -m0644 debian/.debhelper/generated/spaln/dh_installchangelogs.dch.trimmed debian/spaln/usr/share/doc/spaln/changelog.Debian install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/.debhelper/generated/spaln-data/dh_installchangelogs.dch.trimmed debian/spaln-data/usr/share/doc/spaln-data/changelog.Debian dh_installman -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./sortgrcd.1 debian/spaln/usr/share/man/man1/sortgrcd.1 install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./spaln.1 debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/spaln.1.dh-new debian/spaln/usr/share/man/man1/spaln.1 chmod 0644 -- debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- debian/spaln/usr/share/man/man1/sortgrcd.1 dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src mv debian/spaln-data.substvars.new debian/spaln-data.substvars dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src Using 1707770215 as canonical time Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.faa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.cf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc_g.gf.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--sourcedirectory=src cd debian/spaln cd debian/spaln-data chmod a-x usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 chmod a-x usr/share/doc/spaln-data/changelog.Debian gzip -9nf usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 gzip -9nf usr/share/doc/spaln-data/changelog.Debian cd '/build/reproducible-path/spaln-3.0.2+dfsg' cd '/build/reproducible-path/spaln-3.0.2+dfsg' dh_fixperms -O--sourcedirectory=src find debian/spaln ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/spaln-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -- debian/spaln/usr/bin/compild debian/spaln/usr/bin/decompild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/fitild debian/spaln/usr/bin/kmers debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/npssm debian/spaln/usr/bin/plotild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln debian/spaln/usr/bin/utn objcopy --compress-debug-sections debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug chmod 0644 -- debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug dh_strip -a -O--sourcedirectory=src install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makdbs objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/kmers debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/kmers objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug debian/spaln/usr/bin/kmers install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/spaln objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/dvn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/dvn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug debian/spaln/usr/bin/dvn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/fitild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/fitild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug debian/spaln/usr/bin/fitild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/compild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/compild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug debian/spaln/usr/bin/compild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/exinpot debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/exinpot objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug debian/spaln/usr/bin/exinpot install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/utn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/utn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug debian/spaln/usr/bin/utn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/plotild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/plotild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug debian/spaln/usr/bin/plotild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makmdm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug debian/spaln/usr/bin/makmdm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/decompild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/decompild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug debian/spaln/usr/bin/decompild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/rdn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/rdn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug debian/spaln/usr/bin/rdn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/sortgrcd objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/npssm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/npssm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug debian/spaln/usr/bin/npssm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/spaln/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/spaln/usr/lib/debug install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/share/doc ln -s spaln debian/.debhelper/spaln/dbgsym-root/usr/share/doc/spaln-dbgsym install -m0755 -d debian/.debhelper/spaln dh_makeshlibs -a -O--sourcedirectory=src rm -f debian/spaln/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN dpkg-shlibdeps -Tdebian/spaln.substvars debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/kmers debian/spaln/usr/bin/spaln debian/spaln/usr/bin/dvn debian/spaln/usr/bin/fitild debian/spaln/usr/bin/compild debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/utn debian/spaln/usr/bin/plotild debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/decompild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/npssm dh_installdeb -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN dh_gencontrol -O--sourcedirectory=src install -m0755 -d debian/spaln-data/DEBIAN echo misc:Depends= >> debian/spaln-data.substvars echo misc:Pre-Depends= >> debian/spaln-data.substvars dpkg-gencontrol -pspaln-data -ldebian/changelog -Tdebian/spaln-data.substvars -cdebian/control -Pdebian/spaln-data install -m0755 -d debian/spaln/DEBIAN echo misc:Depends= >> debian/spaln.substvars echo misc:Pre-Depends= >> debian/spaln.substvars install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=070ac648f6f60726285b78e733193505dd0ac3ef 1348c45ca8995d1c30fb7c902c327329b4578b21 1ce3b7e2ae0fd8793b7e04ad05cbd62cc0493655 3450d322f0e37b119842690ac80452a5fc686a00 3c3303bdc3af07eadabde6033d11f099593bcbe3 5586fef186af78965ee257b0bcb5cc4a7fba9d17 66313a39ff6d3953891b4569bcbd17851e765868 689dcc00122bec624cd104a5450a08d5001b9e88 95b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4 9c08c35d4a3b17f4727b2956ebef81c3a87d5671 abcae5f323398b73002b9bcc0214cb0cfe30d511 ca6bbb6041eee4fbdb193cf3d029c858c673c998 e5ea39d23dc4e5fac196424f8754987784c46e51 ea32f5007eff9fb98ed92ce0436ed02987f56e74" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/control dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/spaln dpkg-gencontrol: warning: package spaln-data: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/spaln-data/DEBIAN/control chmod 0644 -- debian/spaln/DEBIAN/control dh_md5sums -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN cd debian/spaln >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/spaln-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/spaln/DEBIAN/md5sums install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN cd debian/.debhelper/spaln/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/spaln-data/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src dpkg-deb --root-owner-group --build debian/spaln .. dpkg-deb --root-owner-group --build debian/.debhelper/spaln/dbgsym-root .. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln' in '../spaln_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-dbgsym' in '../spaln-dbgsym_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_3.0.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_3.0.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_3.0.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3405471 and its subdirectories I: Current time: Mon Feb 9 16:16:38 -12 2026 I: pbuilder-time-stamp: 1770696998 Tue Jan 7 21:53:40 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Jan 7 21:53:40 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Jan 7 21:53:40 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Jan 7 21:53:40 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-rUwajX' ==================================================================================== Tue Jan 7 21:53:42 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 spaln unstable /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX 3.0.2+dfsg-2" as arguments. Tue Jan 7 21:53:42 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Tooh9bpp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 7 21:53:42 UTC 2025 I: Downloading source for unstable/spaln=3.0.2+dfsg-2 Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (59.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (59.6 MB/s) Download complete and in download only mode ============================================================================= Re-Building spaln in unstable on amd64 on ionos11-amd64 now. Date: Tue Jan 7 21:53:43 UTC 2025 Date UTC: Tue Jan 7 21:53:43 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/pbuilderrc_qrAq + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' spaln = debian-installer -o spaln = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' spaln = u-boot ']' + case "${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.9qh6YiaX/pbuilderrc_qrAq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b2 --logfile b2/build.log spaln_3.0.2+dfsg-2.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: Wed Jan 8 11:53:43 +14 2025 I: pbuilder-time-stamp: 1736286823 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spaln_3.0.2+dfsg-2.dsc] I: copying [./spaln_3.0.2+dfsg.orig.tar.xz] I: copying [./spaln_3.0.2+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spaln_3.0.2+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting spaln in spaln-3.0.2+dfsg dpkg-source: info: unpacking spaln_3.0.2+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_3.0.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying add_path_to_testscript.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4168590/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 7 21:54 /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/4168590/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4168590/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=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=a0b9d9d6e00e4fcabe3e708dda44a108 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=4168590 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.9qh6YiaX/pbuilderrc_qrAq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b2 --logfile b2/build.log spaln_3.0.2+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) 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/4168590/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), zlib1g-dev, libgsl-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 ... 19848 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 90.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-14 [92.1 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 23.6 MB in 10s (2349 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 ... 19848 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_0.22.5-4_amd64.deb ... Unpacking gettext-base (0.22.5-4) ... 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_2.40.2-14_amd64.deb ... Unpacking bsdextrautils (2.40.2-14) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64: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_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... 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_0.22.5-4_amd64.deb ... Unpacking gettext (0.22.5-4) ... 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_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../30-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../31-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../33-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-14) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-4) ... 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 (0.22.5-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... 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 libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... 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 (13.23) ... Processing triggers for libc-bin (2.40-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/4168590/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/4168590/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/spaln-3.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spaln_3.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 3.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/spaln.substvars debian/spaln-data.substvars debian/files rm -fr -- debian/spaln/ debian/tmp/ debian/spaln-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" exec_prefix=/usr/bin table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb ./configure OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic binaries install to /usr/bin tables install to /usr/share/spaln/table alndbs install to /usr/share/spaln/seqdb wrote Makefile wrote files OK. try make and make install. good luck! make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j20 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c dbs.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gaps.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c divseq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gsinfo.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2d1.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2h1.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2s1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c bitpat.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c seq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c simmtx.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sqpr.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utilseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c vmf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c wln.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c boyer_moore.cc 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++ 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++ 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++ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:483:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 483 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 484 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c clib.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c iolib.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c mfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sets.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c supprime.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc clib.a clib.o iolib.o mfile.o sets.o supprime.o x86_64-linux-gnu-ranlib clib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc sblib.a aln2.o dbs.o gaps.o codepot.o divseq.o gsinfo.o \ fwd2b1.o fwd2d1.o fwd2h1.o fwd2s1.o bitpat.o eijunc.o \ seq.o simmtx.o sqpr.o utilseq.o vmf.o wln.o boyer_moore.o x86_64-linux-gnu-ranlib sblib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o spaln spaln.cc blksrc.o sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o sortgrcd sortgrcd.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now 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++ sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:999:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 999 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.isra': spaln.cc:858:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 858 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'match_2', inlined from 'spaln_job' at spaln.cc:1142:14: spaln.cc:764:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 764 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new: In function 'spaln_job': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j20 test "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c autocomp.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c extcds.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c montseq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c pattern.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c resite.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o exinpot exinpot.cc sblib.a clib.a -lpthread -lm -lz cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o kmers kmers.cc sblib.a clib.a -lpthread -lm -lz cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o npssm npssm.cc sblib.a clib.a -lpthread -lm -lz cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utn.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c ildpdf.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c decompild.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fitild.cc 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++ x86_64-linux-gnu-ar rc ublib.a autocomp.o extcds.o \ montseq.o pattern.o resite.o x86_64-linux-gnu-ranlib ublib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o dvn dvn.cc ublib.a sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o rdn rdn.cc ublib.a sblib.a clib.a -lpthread -lm -lz 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o fitild -DMAIN fitild.cc ildpdf.o clib.a -lpthread -lm -lz \ -L/usr/local/lib -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o compild compild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o decompild decompild.o ildpdf.o fitild.o clib.a -lpthread -lm -lz -lgsl -lgslcblas 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o plotild plotild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ plotild.cc: In function 'getiprms': plotild.cc:136:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 136 | IldPrm* ipprm = new IldPrm[nn + nprm + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o utn utn.o ublib.a sblib.a clib.a -lpthread -lm -lz please make install before test make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-tGgni_pC create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src rm -f -- debian/spaln.substvars debian/spaln-data.substvars rm -fr -- debian/.debhelper/generated/spaln/ debian/spaln/ debian/tmp/ debian/.debhelper/generated/spaln-data/ debian/spaln-data/ rm -f debian/spaln-data.debhelper.log debian/spaln.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_install -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin install -m0755 -d /build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp cd src && make -j20 install DESTDIR=/build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin if [ -s spaln ]; then\ cp spaln sortgrcd makmdm makdbs /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s exinpot ]; then \ cp dvn exinpot kmers npssm rdn utn /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s fitild ]; then \ cp fitild compild decompild plotild /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table ./makmdm /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table 7.6862 5.1057 4.2546 5.1269 2.0279 4.1061 6.1820 7.4714 2.2983 5.2569 9.1111 5.9498 2.3414 4.0530 5.0532 6.8225 5.8518 1.4336 3.2303 6.6374 Pam = 0 Norl fact = 106.899 trace = 106.899 Pam = 10 Norl fact = 13.996 trace = 41.995 Pam = 20 Norl fact = 15.588 trace = 45.299 Pam = 30 Norl fact = 16.894 trace = 47.531 Pam = 40 Norl fact = 18.094 trace = 49.266 Pam = 50 Norl fact = 19.249 trace = 50.701 Pam = 60 Norl fact = 20.386 trace = 51.928 Pam = 70 Norl fact = 21.522 trace = 52.997 Pam = 80 Norl fact = 22.667 trace = 53.943 Pam = 90 Norl fact = 23.828 trace = 54.788 Pam = 100 Norl fact = 25.012 trace = 55.547 Pam = 110 Norl fact = 26.222 trace = 56.234 Pam = 120 Norl fact = 27.462 trace = 56.858 Pam = 130 Norl fact = 28.735 trace = 57.427 Pam = 140 Norl fact = 30.044 trace = 57.946 Pam = 150 Norl fact = 31.391 trace = 58.421 Pam = 160 Norl fact = 32.778 trace = 58.858 Pam = 170 Norl fact = 34.208 trace = 59.259 Pam = 180 Norl fact = 35.683 trace = 59.629 Pam = 190 Norl fact = 37.204 trace = 59.970 Pam = 200 Norl fact = 38.774 trace = 60.286 Pam = 210 Norl fact = 40.394 trace = 60.580 Pam = 220 Norl fact = 42.066 trace = 60.854 Pam = 230 Norl fact = 43.793 trace = 61.110 Pam = 240 Norl fact = 45.577 trace = 61.350 Pam = 250 Norl fact = 47.419 trace = 61.576 Pam = 260 Norl fact = 49.322 trace = 61.791 Pam = 270 Norl fact = 51.287 trace = 61.996 Pam = 280 Norl fact = 53.318 trace = 62.191 Pam = 290 Norl fact = 55.415 trace = 62.380 Pam = 300 Norl fact = 57.582 trace = 62.563 test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_install -O--sourcedirectory=src install -m0755 -d debian/spaln//usr cp --reflink=auto -a debian/tmp/usr/bin debian/spaln//usr/ install -m0755 -d debian/spaln-data//usr cp --reflink=auto -a debian/tmp/usr/share debian/spaln-data//usr/ dh_installdocs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -m0755 -d debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./README.md debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/README.test debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/tests/run-unit-test debian/spaln/usr/share/doc/spaln chmod -R u\+rw,go=rX debian/spaln/usr/share/doc install -p -m0644 debian/README.Debian debian/spaln/usr/share/doc/spaln/README.Debian install -p -m0644 debian/copyright debian/spaln/usr/share/doc/spaln/copyright install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/copyright debian/spaln-data/usr/share/doc/spaln-data/copyright dh_installchangelogs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -p -m0644 debian/.debhelper/generated/spaln/dh_installchangelogs.dch.trimmed debian/spaln/usr/share/doc/spaln/changelog.Debian install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/.debhelper/generated/spaln-data/dh_installchangelogs.dch.trimmed debian/spaln-data/usr/share/doc/spaln-data/changelog.Debian dh_installman -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./sortgrcd.1 debian/spaln/usr/share/man/man1/sortgrcd.1 install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./spaln.1 debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 mv debian/spaln/usr/share/man/man1/spaln.1.dh-new debian/spaln/usr/share/man/man1/spaln.1 chmod 0644 -- debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- debian/spaln/usr/share/man/man1/sortgrcd.1 dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src mv debian/spaln-data.substvars.new debian/spaln-data.substvars dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src Using 1707770215 as canonical time Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.faa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.cf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc_g.gf.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--sourcedirectory=src cd debian/spaln cd debian/spaln-data chmod a-x usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 chmod a-x usr/share/doc/spaln-data/changelog.Debian gzip -9nf usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 gzip -9nf usr/share/doc/spaln-data/changelog.Debian cd '/build/reproducible-path/spaln-3.0.2+dfsg' cd '/build/reproducible-path/spaln-3.0.2+dfsg' dh_fixperms -O--sourcedirectory=src find debian/spaln-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln-data/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -- debian/spaln/usr/bin/compild debian/spaln/usr/bin/decompild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/fitild debian/spaln/usr/bin/kmers debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/npssm debian/spaln/usr/bin/plotild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln debian/spaln/usr/bin/utn objcopy --compress-debug-sections debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug chmod 0644 -- debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug dh_strip -a -O--sourcedirectory=src install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/npssm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/npssm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug debian/spaln/usr/bin/npssm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/exinpot debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/exinpot objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug debian/spaln/usr/bin/exinpot install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/decompild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/decompild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug debian/spaln/usr/bin/decompild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/utn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/utn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug debian/spaln/usr/bin/utn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/compild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/compild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug debian/spaln/usr/bin/compild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/fitild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/fitild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug debian/spaln/usr/bin/fitild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/dvn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/dvn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug debian/spaln/usr/bin/dvn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/spaln objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makdbs objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/sortgrcd objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/kmers debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/kmers objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug debian/spaln/usr/bin/kmers install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/rdn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/rdn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug debian/spaln/usr/bin/rdn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/plotild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/plotild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug debian/spaln/usr/bin/plotild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makmdm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug debian/spaln/usr/bin/makmdm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/spaln/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/spaln/usr/lib/debug install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/share/doc ln -s spaln debian/.debhelper/spaln/dbgsym-root/usr/share/doc/spaln-dbgsym install -m0755 -d debian/.debhelper/spaln dh_makeshlibs -a -O--sourcedirectory=src rm -f debian/spaln/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN dpkg-shlibdeps -Tdebian/spaln.substvars debian/spaln/usr/bin/npssm debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/decompild debian/spaln/usr/bin/utn debian/spaln/usr/bin/compild debian/spaln/usr/bin/fitild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/spaln debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/kmers debian/spaln/usr/bin/rdn debian/spaln/usr/bin/plotild debian/spaln/usr/bin/makmdm dh_installdeb -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN dh_gencontrol -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN echo misc:Depends= >> debian/spaln.substvars echo misc:Pre-Depends= >> debian/spaln.substvars install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=070ac648f6f60726285b78e733193505dd0ac3ef 1348c45ca8995d1c30fb7c902c327329b4578b21 1ce3b7e2ae0fd8793b7e04ad05cbd62cc0493655 3450d322f0e37b119842690ac80452a5fc686a00 3c3303bdc3af07eadabde6033d11f099593bcbe3 5586fef186af78965ee257b0bcb5cc4a7fba9d17 66313a39ff6d3953891b4569bcbd17851e765868 689dcc00122bec624cd104a5450a08d5001b9e88 95b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4 9c08c35d4a3b17f4727b2956ebef81c3a87d5671 abcae5f323398b73002b9bcc0214cb0cfe30d511 ca6bbb6041eee4fbdb193cf3d029c858c673c998 e5ea39d23dc4e5fac196424f8754987784c46e51 ea32f5007eff9fb98ed92ce0436ed02987f56e74" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/spaln-data/DEBIAN echo misc:Depends= >> debian/spaln-data.substvars echo misc:Pre-Depends= >> debian/spaln-data.substvars dpkg-gencontrol -pspaln-data -ldebian/changelog -Tdebian/spaln-data.substvars -cdebian/control -Pdebian/spaln-data dpkg-gencontrol: warning: package spaln-data: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/spaln-data/DEBIAN/control chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/control dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/spaln chmod 0644 -- debian/spaln/DEBIAN/control dh_md5sums -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN cd debian/spaln >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/spaln-data/DEBIAN cd debian/spaln-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/spaln/DEBIAN/md5sums install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN cd debian/.debhelper/spaln/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/spaln-data/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src dpkg-deb --root-owner-group --build debian/spaln .. dpkg-deb --root-owner-group --build debian/.debhelper/spaln/dbgsym-root .. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln-dbgsym' in '../spaln-dbgsym_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln' in '../spaln_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_3.0.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_3.0.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_3.0.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4168590/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4168590/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/4168590 and its subdirectories I: Current time: Wed Jan 8 12:01:53 +14 2025 I: pbuilder-time-stamp: 1736287313 + false + set +x Tue Jan 7 22:01:53 UTC 2025 I: Signing ./b2/spaln_3.0.2+dfsg-2_amd64.buildinfo as spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Jan 7 22:01:53 UTC 2025 I: Signed ./b2/spaln_3.0.2+dfsg-2_amd64.buildinfo as ./b2/spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Jan 7 22:01:53 UTC 2025 - build #2 for spaln/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Tue Jan 7 22:01:53 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Tooh9bpp, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX: total 88 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 21:53 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 22:01 b2 -rw------- 1 jenkins jenkins 72137 Jan 7 21:53 rbuildlog.K7fv954 -rw-r--r-- 1 jenkins jenkins 2224 Feb 12 2024 spaln_3.0.2+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1: total 23204 -rw-r--r-- 1 jenkins jenkins 68512 Jan 7 21:53 build.log -rw-r--r-- 1 jenkins jenkins 19478864 Jan 7 21:53 spaln-data_3.0.2+dfsg-2_all.deb -rw-r--r-- 1 jenkins jenkins 3553100 Jan 7 21:53 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 6124 Jan 7 21:53 spaln_3.0.2+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2224 Jan 7 21:53 spaln_3.0.2+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5397 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6279 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1771 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 580300 Jan 7 21:53 spaln_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1258 Jan 7 21:53 spaln_3.0.2+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b2: total 23172 -rw-r--r-- 1 jenkins jenkins 70433 Jan 7 22:01 build.log -rw-r--r-- 1 jenkins jenkins 19478864 Jan 7 22:01 spaln-data_3.0.2+dfsg-2_all.deb -rw-r--r-- 1 jenkins jenkins 3553100 Jan 7 22:01 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 6124 Jan 7 22:01 spaln_3.0.2+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2224 Jan 7 22:01 spaln_3.0.2+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5386 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6268 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1771 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 580300 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1258 Jan 7 22:01 spaln_3.0.2+dfsg-2_source.changes Tue Jan 7 22:01:54 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Jan 7 22:01:55 UTC 2025 I: spaln_3.0.2+dfsg-2_amd64.changes: Format: 1.8 Date: Mon, 12 Feb 2024 21:36:55 +0100 Source: spaln Binary: spaln spaln-data spaln-dbgsym Architecture: all amd64 Version: 3.0.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: spaln - splicing-aware transcript-alignment to genomic DNA spaln-data - splicing-aware transcript-alignment to genomic DNA (data) Closes: 1063798 Changes: spaln (3.0.2+dfsg-2) unstable; urgency=medium . * Team upload. * Fix portability for arm64 Closes: #1063798 Checksums-Sha1: aafe1f28cb7f7c5ec49edf5846d3ca136ad46d4b 19478864 spaln-data_3.0.2+dfsg-2_all.deb b79a5f60242fa46bc652b46c6c30393552ae505a 3553100 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb 0295ebd83740abf70e0cc2f8c4d7229881f9547f 5397 spaln_3.0.2+dfsg-2_amd64.buildinfo 9c03e099bc6cd08744ef0340a32f32e48e167c4a 580300 spaln_3.0.2+dfsg-2_amd64.deb Checksums-Sha256: fa2c9f24c178e069005330e59f33443a79c7a962d0de31c9da08420298a6e09b 19478864 spaln-data_3.0.2+dfsg-2_all.deb 356a02ec52297a7161ed964eb3910c8a9c8e37280199e7849ebfa671f6ab36bf 3553100 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb 8e4322755391bc4192d1f5caa9ba7db8ba1d9f8db510777be9371bc845507290 5397 spaln_3.0.2+dfsg-2_amd64.buildinfo 67fe9e3eef1caf591cb37a12595e34656dc24b7357aee4a994e4f20f807c4dd4 580300 spaln_3.0.2+dfsg-2_amd64.deb Files: 87ca3a8b817c4ea176f11d634a55be93 19478864 science optional spaln-data_3.0.2+dfsg-2_all.deb 9815b6c1605c8b51d524cc80d645c854 3553100 debug optional spaln-dbgsym_3.0.2+dfsg-2_amd64.deb b6c2005b95ba889ef271c118af969995 5397 science optional spaln_3.0.2+dfsg-2_amd64.buildinfo afd4383f018ab081a62760706e416ed0 580300 science optional spaln_3.0.2+dfsg-2_amd64.deb 12,13c12,13 < bsdextrautils (= 2.40.2-13), < bsdutils (= 1:2.40.2-13), --- > bsdextrautils (= 2.40.2-14), > bsdutils (= 1:2.40.2-14), 58c58 < libblkid1 (= 2.40.2-13), --- > libblkid1 (= 2.40.2-14), 97c97 < libmount1 (= 2.40.2-13), --- > libmount1 (= 2.40.2-14), 111c111 < libsmartcols1 (= 2.40.2-13), --- > libsmartcols1 (= 2.40.2-14), 123c123 < libuuid1 (= 2.40.2-13), --- > libuuid1 (= 2.40.2-14), 144c144 < util-linux (= 2.40.2-13), --- > util-linux (= 2.40.2-14), ============================================================================= Tue Jan 7 22:01:55 UTC 2025 - The installed build depends vary according to the two .buildinfo files, probably due to mirror updates. Doing the first build on ionos5-amd64.debian.net again. ============================================================================= Tue Jan 7 22:01:55 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Jan 7 22:01:55 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Tue Jan 7 22:01:55 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Fltx5x' ==================================================================================== Tue Feb 10 04:24:56 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 spaln unstable /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX 3.0.2+dfsg-2" as arguments. Tue Feb 10 04:24:56 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-WXrRQpHY" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Feb 10 04:24:56 UTC 2026 I: Downloading source for unstable/spaln=3.0.2+dfsg-2 Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (138 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'spaln' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spaln.git Please use: git clone https://salsa.debian.org/med-team/spaln.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 19.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (dsc) [2224 B] Get:2 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (tar) [19.8 MB] Get:3 http://deb.debian.org/debian unstable/main spaln 3.0.2+dfsg-2 (diff) [6124 B] Fetched 19.8 MB in 0s (138 MB/s) Download complete and in download only mode ============================================================================= Building spaln in unstable on amd64 on ionos5-amd64 now. Date: Tue Feb 10 04:24:56 UTC 2026 Date UTC: Tue Feb 10 04:24:56 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 9 16:24:56 -12 2026 I: pbuilder-time-stamp: 1770697496 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spaln_3.0.2+dfsg-2.dsc] I: copying [./spaln_3.0.2+dfsg.orig.tar.xz] I: copying [./spaln_3.0.2+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spaln_3.0.2+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting spaln in spaln-3.0.2+dfsg dpkg-source: info: unpacking spaln_3.0.2+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_3.0.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying add_path_to_testscript.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3474203/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='84899bb2f0e04e76afe491f31bad0b72' 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='3474203' 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.9qh6YiaX/pbuilderrc_BMz6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1 --logfile b1/build.log spaln_3.0.2+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3474203/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), zlib1g-dev, libgsl-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 ... 19848 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 90.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-13 [91.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 23.6 MB in 1s (19.2 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 ... 19848 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_0.22.5-4_amd64.deb ... Unpacking gettext-base (0.22.5-4) ... 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_2.40.2-13_amd64.deb ... Unpacking bsdextrautils (2.40.2-13) ... Selecting previously unselected package libpipeline1:amd64. 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... 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_0.22.5-4_amd64.deb ... Unpacking gettext (0.22.5-4) ... 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Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... 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 (13.23) ... Processing triggers for libc-bin (2.40-5) ... 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/spaln-3.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spaln_3.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 3.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/spaln.substvars debian/spaln-data.substvars debian/files rm -fr -- debian/spaln/ debian/tmp/ debian/spaln-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" exec_prefix=/usr/bin table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb ./configure OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic binaries install to /usr/bin tables install to /usr/share/spaln/table alndbs install to /usr/share/spaln/seqdb wrote Makefile wrote files OK. try make and make install. good luck! make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j42 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gaps.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c divseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gsinfo.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2d1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2h1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2s1.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c bitpat.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c seq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c simmtx.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sqpr.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utilseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c vmf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c wln.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c boyer_moore.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c clib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c iolib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c mfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sets.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c supprime.cc 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++ 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++ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:483:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 483 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 484 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* x86_64-linux-gnu-ar rc clib.a clib.o iolib.o mfile.o sets.o supprime.o x86_64-linux-gnu-ranlib clib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc sblib.a aln2.o dbs.o gaps.o codepot.o divseq.o gsinfo.o \ fwd2b1.o fwd2d1.o fwd2h1.o fwd2s1.o bitpat.o eijunc.o \ seq.o simmtx.o sqpr.o utilseq.o vmf.o wln.o boyer_moore.o x86_64-linux-gnu-ranlib sblib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o spaln spaln.cc blksrc.o sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o sortgrcd sortgrcd.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now 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++ sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:999:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 999 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.isra': spaln.cc:858:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 858 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'match_2', inlined from 'spaln_job' at spaln.cc:1142:14: spaln.cc:764:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 764 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new: In function 'spaln_job': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c autocomp.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c extcds.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c montseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c pattern.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c resite.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o exinpot exinpot.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o kmers kmers.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o npssm npssm.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utn.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c ildpdf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c decompild.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fitild.cc 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++ 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++ 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++ x86_64-linux-gnu-ar rc ublib.a autocomp.o extcds.o \ montseq.o pattern.o resite.o x86_64-linux-gnu-ranlib ublib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o dvn dvn.cc ublib.a sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o rdn rdn.cc ublib.a sblib.a clib.a -lpthread -lm -lz 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o fitild -DMAIN fitild.cc ildpdf.o clib.a -lpthread -lm -lz \ -L/usr/local/lib -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o compild compild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o decompild decompild.o ildpdf.o fitild.o clib.a -lpthread -lm -lz -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o plotild plotild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas 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++ plotild.cc: In function 'getiprms': plotild.cc:136:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 136 | IldPrm* ipprm = new IldPrm[nn + nprm + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o utn utn.o ublib.a sblib.a clib.a -lpthread -lm -lz please make install before test make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-3yYwjW7M create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src rm -f -- debian/spaln.substvars debian/spaln-data.substvars rm -fr -- debian/.debhelper/generated/spaln/ debian/spaln/ debian/tmp/ debian/.debhelper/generated/spaln-data/ debian/spaln-data/ rm -f debian/spaln-data.debhelper.log debian/spaln.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_install -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin install -m0755 -d /build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp cd src && make -j42 install DESTDIR=/build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin if [ -s spaln ]; then\ cp spaln sortgrcd makmdm makdbs /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s exinpot ]; then \ cp dvn exinpot kmers npssm rdn utn /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s fitild ]; then \ cp fitild compild decompild plotild /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table ./makmdm /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table 7.6862 5.1057 4.2546 5.1269 2.0279 4.1061 6.1820 7.4714 2.2983 5.2569 9.1111 5.9498 2.3414 4.0530 5.0532 6.8225 5.8518 1.4336 3.2303 6.6374 Pam = 0 Norl fact = 106.899 trace = 106.899 Pam = 10 Norl fact = 13.996 trace = 41.995 Pam = 20 Norl fact = 15.588 trace = 45.299 Pam = 30 Norl fact = 16.894 trace = 47.531 Pam = 40 Norl fact = 18.094 trace = 49.266 Pam = 50 Norl fact = 19.249 trace = 50.701 Pam = 60 Norl fact = 20.386 trace = 51.928 Pam = 70 Norl fact = 21.522 trace = 52.997 Pam = 80 Norl fact = 22.667 trace = 53.943 Pam = 90 Norl fact = 23.828 trace = 54.788 Pam = 100 Norl fact = 25.012 trace = 55.547 Pam = 110 Norl fact = 26.222 trace = 56.234 Pam = 120 Norl fact = 27.462 trace = 56.858 Pam = 130 Norl fact = 28.735 trace = 57.427 Pam = 140 Norl fact = 30.044 trace = 57.946 Pam = 150 Norl fact = 31.391 trace = 58.421 Pam = 160 Norl fact = 32.778 trace = 58.858 Pam = 170 Norl fact = 34.208 trace = 59.259 Pam = 180 Norl fact = 35.683 trace = 59.629 Pam = 190 Norl fact = 37.204 trace = 59.970 Pam = 200 Norl fact = 38.774 trace = 60.286 Pam = 210 Norl fact = 40.394 trace = 60.580 Pam = 220 Norl fact = 42.066 trace = 60.854 Pam = 230 Norl fact = 43.793 trace = 61.110 Pam = 240 Norl fact = 45.577 trace = 61.350 Pam = 250 Norl fact = 47.419 trace = 61.576 Pam = 260 Norl fact = 49.322 trace = 61.791 Pam = 270 Norl fact = 51.287 trace = 61.996 Pam = 280 Norl fact = 53.318 trace = 62.191 Pam = 290 Norl fact = 55.415 trace = 62.380 Pam = 300 Norl fact = 57.582 trace = 62.563 test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_install -O--sourcedirectory=src install -m0755 -d debian/spaln//usr cp --reflink=auto -a debian/tmp/usr/bin debian/spaln//usr/ install -m0755 -d debian/spaln-data//usr cp --reflink=auto -a debian/tmp/usr/share debian/spaln-data//usr/ dh_installdocs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -m0755 -d debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./README.md debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/README.test debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/tests/run-unit-test debian/spaln/usr/share/doc/spaln chmod -R u\+rw,go=rX debian/spaln/usr/share/doc install -p -m0644 debian/README.Debian debian/spaln/usr/share/doc/spaln/README.Debian install -p -m0644 debian/copyright debian/spaln/usr/share/doc/spaln/copyright install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/copyright debian/spaln-data/usr/share/doc/spaln-data/copyright dh_installchangelogs -O--sourcedirectory=src install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/.debhelper/generated/spaln-data/dh_installchangelogs.dch.trimmed debian/spaln-data/usr/share/doc/spaln-data/changelog.Debian install -m0755 -d debian/spaln/usr/share/doc/spaln install -p -m0644 debian/.debhelper/generated/spaln/dh_installchangelogs.dch.trimmed debian/spaln/usr/share/doc/spaln/changelog.Debian dh_installman -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./sortgrcd.1 debian/spaln/usr/share/man/man1/sortgrcd.1 install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./spaln.1 debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/spaln.1.dh-new debian/spaln/usr/share/man/man1/spaln.1 chmod 0644 -- debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- debian/spaln/usr/share/man/man1/sortgrcd.1 dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src mv debian/spaln-data.substvars.new debian/spaln-data.substvars dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src Using 1707770215 as canonical time Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.faa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.cf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc_g.gf.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--sourcedirectory=src cd debian/spaln cd debian/spaln-data chmod a-x usr/share/doc/spaln-data/changelog.Debian chmod a-x usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 gzip -9nf usr/share/doc/spaln-data/changelog.Debian gzip -9nf usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 cd '/build/reproducible-path/spaln-3.0.2+dfsg' cd '/build/reproducible-path/spaln-3.0.2+dfsg' dh_fixperms -O--sourcedirectory=src find debian/spaln ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/spaln-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -- debian/spaln/usr/bin/compild debian/spaln/usr/bin/decompild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/fitild debian/spaln/usr/bin/kmers debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/npssm debian/spaln/usr/bin/plotild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln debian/spaln/usr/bin/utn objcopy --compress-debug-sections debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug chmod 0644 -- debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug dh_strip -a -O--sourcedirectory=src install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makdbs objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/kmers debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/kmers objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug debian/spaln/usr/bin/kmers install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/spaln objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/dvn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/dvn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug debian/spaln/usr/bin/dvn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/fitild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/fitild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug debian/spaln/usr/bin/fitild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/compild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/compild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug debian/spaln/usr/bin/compild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/exinpot debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/exinpot objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug debian/spaln/usr/bin/exinpot install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/utn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/utn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug debian/spaln/usr/bin/utn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/plotild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/plotild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug debian/spaln/usr/bin/plotild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makmdm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug debian/spaln/usr/bin/makmdm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/decompild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/decompild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug debian/spaln/usr/bin/decompild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/rdn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/rdn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug debian/spaln/usr/bin/rdn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/sortgrcd objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/npssm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/npssm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug debian/spaln/usr/bin/npssm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/spaln/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/spaln/usr/lib/debug install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/share/doc ln -s spaln debian/.debhelper/spaln/dbgsym-root/usr/share/doc/spaln-dbgsym install -m0755 -d debian/.debhelper/spaln dh_makeshlibs -a -O--sourcedirectory=src rm -f debian/spaln/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN dpkg-shlibdeps -Tdebian/spaln.substvars debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/kmers debian/spaln/usr/bin/spaln debian/spaln/usr/bin/dvn debian/spaln/usr/bin/fitild debian/spaln/usr/bin/compild debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/utn debian/spaln/usr/bin/plotild debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/decompild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/npssm dh_installdeb -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN dh_gencontrol -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN echo misc:Depends= >> debian/spaln.substvars echo misc:Pre-Depends= >> debian/spaln.substvars install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=070ac648f6f60726285b78e733193505dd0ac3ef 1348c45ca8995d1c30fb7c902c327329b4578b21 1ce3b7e2ae0fd8793b7e04ad05cbd62cc0493655 3450d322f0e37b119842690ac80452a5fc686a00 3c3303bdc3af07eadabde6033d11f099593bcbe3 5586fef186af78965ee257b0bcb5cc4a7fba9d17 66313a39ff6d3953891b4569bcbd17851e765868 689dcc00122bec624cd104a5450a08d5001b9e88 95b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4 9c08c35d4a3b17f4727b2956ebef81c3a87d5671 abcae5f323398b73002b9bcc0214cb0cfe30d511 ca6bbb6041eee4fbdb193cf3d029c858c673c998 e5ea39d23dc4e5fac196424f8754987784c46e51 ea32f5007eff9fb98ed92ce0436ed02987f56e74" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/spaln-data/DEBIAN echo misc:Depends= >> debian/spaln-data.substvars echo misc:Pre-Depends= >> debian/spaln-data.substvars dpkg-gencontrol -pspaln-data -ldebian/changelog -Tdebian/spaln-data.substvars -cdebian/control -Pdebian/spaln-data chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/control dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/spaln dpkg-gencontrol: warning: package spaln-data: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/spaln-data/DEBIAN/control chmod 0644 -- debian/spaln/DEBIAN/control dh_md5sums -O--sourcedirectory=src install -m0755 -d debian/spaln-data/DEBIAN install -m0755 -d debian/spaln/DEBIAN cd debian/spaln >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/spaln-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/spaln/DEBIAN/md5sums install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN cd debian/.debhelper/spaln/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/spaln-data/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src dpkg-deb --root-owner-group --build debian/spaln .. dpkg-deb --root-owner-group --build debian/.debhelper/spaln/dbgsym-root .. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln' in '../spaln_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-dbgsym' in '../spaln-dbgsym_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_3.0.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_3.0.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_3.0.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3474203 and its subdirectories I: Current time: Mon Feb 9 16:26:42 -12 2026 I: pbuilder-time-stamp: 1770697602 Tue Feb 10 04:26:42 UTC 2026 I: Signing ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo as spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Feb 10 04:26:42 UTC 2026 I: Signed ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo as ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo.asc Tue Feb 10 04:26:42 UTC 2026 - build #1 for spaln/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Tue Feb 10 04:26:42 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-WXrRQpHY, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX: total 100 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 22:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 7 22:01 b2 -rw------- 1 jenkins jenkins 74148 Jan 7 22:01 rbuildlog.K7fv954 -rw-r--r-- 1 jenkins jenkins 2224 Feb 12 2024 spaln_3.0.2+dfsg-2.dsc -rw------- 1 jenkins jenkins 4045 Jan 7 22:01 tmp.221A6YDUA6 -rw------- 1 jenkins jenkins 4045 Jan 7 22:01 tmp.w335E3x3zz /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1: total 23204 -rw-r--r-- 1 jenkins jenkins 68512 Jan 7 22:03 build.log -rw-r--r-- 1 jenkins jenkins 19478864 Jan 7 22:03 spaln-data_3.0.2+dfsg-2_all.deb -rw-r--r-- 1 jenkins jenkins 3553100 Jan 7 22:03 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 6124 Jan 7 22:03 spaln_3.0.2+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2224 Jan 7 22:03 spaln_3.0.2+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5397 Jan 7 22:03 spaln_3.0.2+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6279 Jan 7 22:03 spaln_3.0.2+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1771 Jan 7 22:03 spaln_3.0.2+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 580300 Jan 7 22:03 spaln_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1258 Jan 7 22:03 spaln_3.0.2+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b2: total 23208 -rw-r--r-- 1 jenkins jenkins 70433 Jan 7 22:01 build.log -rw-r--r-- 1 jenkins jenkins 19478864 Jan 7 22:01 spaln-data_3.0.2+dfsg-2_all.deb -rw-r--r-- 1 jenkins jenkins 3553100 Jan 7 22:01 spaln-dbgsym_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 6124 Jan 7 22:01 spaln_3.0.2+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2224 Jan 7 22:01 spaln_3.0.2+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5386 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6268 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1771 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 580300 Jan 7 22:01 spaln_3.0.2+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1258 Jan 7 22:01 spaln_3.0.2+dfsg-2_source.changes Tue Jan 7 22:03:42 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 9 16:24:56 -12 2026 I: pbuilder-time-stamp: 1770697496 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spaln_3.0.2+dfsg-2.dsc] I: copying [./spaln_3.0.2+dfsg.orig.tar.xz] I: copying [./spaln_3.0.2+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spaln_3.0.2+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting spaln in spaln-3.0.2+dfsg dpkg-source: info: unpacking spaln_3.0.2+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_3.0.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying add_path_to_testscript.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3474203/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='84899bb2f0e04e76afe491f31bad0b72' 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='3474203' 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.9qh6YiaX/pbuilderrc_BMz6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/b1 --logfile b1/build.log spaln_3.0.2+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3474203/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), zlib1g-dev, libgsl-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 ... 19848 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 90.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-13 [91.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 23.6 MB in 1s (19.2 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 ... 19848 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_0.22.5-4_amd64.deb ... Unpacking gettext-base (0.22.5-4) ... 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_2.40.2-13_amd64.deb ... Unpacking bsdextrautils (2.40.2-13) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... 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_0.22.5-4_amd64.deb ... Unpacking gettext (0.22.5-4) ... 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_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../30-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../31-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../33-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-4) ... 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 (0.22.5-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... 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 libgsl28:amd64 (2.8+dfsg-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... 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 (13.23) ... Processing triggers for libc-bin (2.40-5) ... 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/spaln-3.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spaln_3.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 3.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/spaln.substvars debian/spaln-data.substvars debian/files rm -fr -- debian/spaln/ debian/tmp/ debian/spaln-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" exec_prefix=/usr/bin table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb ./configure OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic binaries install to /usr/bin tables install to /usr/share/spaln/table alndbs install to /usr/share/spaln/seqdb wrote Makefile wrote files OK. try make and make install. good luck! make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j42 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gaps.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c divseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c gsinfo.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2d1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2h1.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fwd2s1.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c bitpat.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c seq.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c simmtx.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sqpr.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utilseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c vmf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c wln.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c boyer_moore.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c clib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c iolib.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c mfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c sets.cc 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c supprime.cc 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++ 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++ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:483:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 483 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 484 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* x86_64-linux-gnu-ar rc clib.a clib.o iolib.o mfile.o sets.o supprime.o x86_64-linux-gnu-ranlib clib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ x86_64-linux-gnu-ar rc sblib.a aln2.o dbs.o gaps.o codepot.o divseq.o gsinfo.o \ fwd2b1.o fwd2d1.o fwd2h1.o fwd2s1.o bitpat.o eijunc.o \ seq.o simmtx.o sqpr.o utilseq.o vmf.o wln.o boyer_moore.o x86_64-linux-gnu-ranlib sblib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o spaln spaln.cc blksrc.o sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o sortgrcd sortgrcd.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now 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++ sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:999:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 999 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.isra': spaln.cc:858:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 858 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'match_2', inlined from 'spaln_job' at spaln.cc:1142:14: spaln.cc:764:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 764 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/14/new: In function 'spaln_job': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c autocomp.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c extcds.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c montseq.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c pattern.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c resite.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o exinpot exinpot.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o kmers kmers.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o npssm npssm.cc sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c utn.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c ildpdf.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c decompild.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -c fitild.cc 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++ 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++ 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++ x86_64-linux-gnu-ar rc ublib.a autocomp.o extcds.o \ montseq.o pattern.o resite.o x86_64-linux-gnu-ranlib ublib.a x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o dvn dvn.cc ublib.a sblib.a clib.a -lpthread -lm -lz x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o rdn rdn.cc ublib.a sblib.a clib.a -lpthread -lm -lz 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++ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o fitild -DMAIN fitild.cc ildpdf.o clib.a -lpthread -lm -lz \ -L/usr/local/lib -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o compild compild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o decompild decompild.o ildpdf.o fitild.o clib.a -lpthread -lm -lz -lgsl -lgslcblas x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o plotild plotild.cc ildpdf.o clib.a -lpthread -lm -lz -lm -lgsl -lgslcblas 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++ plotild.cc: In function 'getiprms': plotild.cc:136:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 136 | IldPrm* ipprm = new IldPrm[nn + nprm + 1]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spaln-3.0.2+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DM_THREAD=1 -o utn utn.o ublib.a sblib.a clib.a -lpthread -lm -lz please make install before test make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-3yYwjW7M create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src rm -f -- debian/spaln.substvars debian/spaln-data.substvars rm -fr -- debian/.debhelper/generated/spaln/ debian/spaln/ debian/tmp/ debian/.debhelper/generated/spaln-data/ debian/spaln-data/ rm -f debian/spaln-data.debhelper.log debian/spaln.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_auto_install -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin install -m0755 -d /build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp cd src && make -j42 install DESTDIR=/build/reproducible-path/spaln-3.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin if [ -s spaln ]; then\ cp spaln sortgrcd makmdm makdbs /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s exinpot ]; then \ cp dvn exinpot kmers npssm rdn utn /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi if [ -s fitild ]; then \ cp fitild compild decompild plotild /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/bin; \ fi test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table ./makmdm /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/table 7.6862 5.1057 4.2546 5.1269 2.0279 4.1061 6.1820 7.4714 2.2983 5.2569 9.1111 5.9498 2.3414 4.0530 5.0532 6.8225 5.8518 1.4336 3.2303 6.6374 Pam = 0 Norl fact = 106.899 trace = 106.899 Pam = 10 Norl fact = 13.996 trace = 41.995 Pam = 20 Norl fact = 15.588 trace = 45.299 Pam = 30 Norl fact = 16.894 trace = 47.531 Pam = 40 Norl fact = 18.094 trace = 49.266 Pam = 50 Norl fact = 19.249 trace = 50.701 Pam = 60 Norl fact = 20.386 trace = 51.928 Pam = 70 Norl fact = 21.522 trace = 52.997 Pam = 80 Norl fact = 22.667 trace = 53.943 Pam = 90 Norl fact = 23.828 trace = 54.788 Pam = 100 Norl fact = 25.012 trace = 55.547 Pam = 110 Norl fact = 26.222 trace = 56.234 Pam = 120 Norl fact = 27.462 trace = 56.858 Pam = 130 Norl fact = 28.735 trace = 57.427 Pam = 140 Norl fact = 30.044 trace = 57.946 Pam = 150 Norl fact = 31.391 trace = 58.421 Pam = 160 Norl fact = 32.778 trace = 58.858 Pam = 170 Norl fact = 34.208 trace = 59.259 Pam = 180 Norl fact = 35.683 trace = 59.629 Pam = 190 Norl fact = 37.204 trace = 59.970 Pam = 200 Norl fact = 38.774 trace = 60.286 Pam = 210 Norl fact = 40.394 trace = 60.580 Pam = 220 Norl fact = 42.066 trace = 60.854 Pam = 230 Norl fact = 43.793 trace = 61.110 Pam = 240 Norl fact = 45.577 trace = 61.350 Pam = 250 Norl fact = 47.419 trace = 61.576 Pam = 260 Norl fact = 49.322 trace = 61.791 Pam = 270 Norl fact = 51.287 trace = 61.996 Pam = 280 Norl fact = 53.318 trace = 62.191 Pam = 290 Norl fact = 55.415 trace = 62.380 Pam = 300 Norl fact = 57.582 trace = 62.563 test -d /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb || mkdir -p /build/reproducible-path/spaln-3.0.2+dfsg/debian/tmp/usr/share/spaln/seqdb make[2]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/spaln-3.0.2+dfsg' dh_install -O--sourcedirectory=src install -m0755 -d debian/spaln//usr cp --reflink=auto -a debian/tmp/usr/bin debian/spaln//usr/ install -m0755 -d debian/spaln-data//usr cp --reflink=auto -a debian/tmp/usr/share debian/spaln-data//usr/ dh_installdocs -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/doc/spaln install -m0755 -d debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./README.md debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/README.test debian/spaln/usr/share/doc/spaln cp --reflink=auto -a ./debian/tests/run-unit-test debian/spaln/usr/share/doc/spaln chmod -R u\+rw,go=rX debian/spaln/usr/share/doc install -p -m0644 debian/README.Debian debian/spaln/usr/share/doc/spaln/README.Debian install -p -m0644 debian/copyright debian/spaln/usr/share/doc/spaln/copyright install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/copyright debian/spaln-data/usr/share/doc/spaln-data/copyright dh_installchangelogs -O--sourcedirectory=src install -m0755 -d debian/spaln-data/usr/share/doc/spaln-data install -p -m0644 debian/.debhelper/generated/spaln-data/dh_installchangelogs.dch.trimmed debian/spaln-data/usr/share/doc/spaln-data/changelog.Debian install -m0755 -d debian/spaln/usr/share/doc/spaln install -p -m0644 debian/.debhelper/generated/spaln/dh_installchangelogs.dch.trimmed debian/spaln/usr/share/doc/spaln/changelog.Debian dh_installman -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./sortgrcd.1 debian/spaln/usr/share/man/man1/sortgrcd.1 install -m0755 -d debian/spaln/usr/share/man/man1/ install -p -m0644 ./spaln.1 debian/spaln/usr/share/man/man1/spaln.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 man-recode --to-code UTF-8 --suffix .dh-new debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/spaln.1.dh-new debian/spaln/usr/share/man/man1/spaln.1 chmod 0644 -- debian/spaln/usr/share/man/man1/spaln.1 mv debian/spaln/usr/share/man/man1/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- debian/spaln/usr/share/man/man1/sortgrcd.1 dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src mv debian/spaln-data.substvars.new debian/spaln-data.substvars dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src Using 1707770215 as canonical time Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.faa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc.cf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/spaln-data/usr/share/spaln/seqdb/dictdisc_g.gf.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--sourcedirectory=src cd debian/spaln cd debian/spaln-data chmod a-x usr/share/doc/spaln-data/changelog.Debian chmod a-x usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 gzip -9nf usr/share/doc/spaln-data/changelog.Debian gzip -9nf usr/share/doc/spaln/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 cd '/build/reproducible-path/spaln-3.0.2+dfsg' cd '/build/reproducible-path/spaln-3.0.2+dfsg' dh_fixperms -O--sourcedirectory=src find debian/spaln ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/spaln/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln-data/usr/share/doc -type f -a -true -a ! -regex 'debian/spaln-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/spaln/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/spaln-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/spaln-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src install -m0755 -d debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug -- debian/spaln/usr/bin/compild debian/spaln/usr/bin/decompild debian/spaln/usr/bin/dvn debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/fitild debian/spaln/usr/bin/kmers debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/npssm debian/spaln/usr/bin/plotild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln debian/spaln/usr/bin/utn objcopy --compress-debug-sections debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug chmod 0644 -- debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu/spaln.debug dh_strip -a -O--sourcedirectory=src install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makdbs objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ea/32f5007eff9fb98ed92ce0436ed02987f56e74.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/kmers debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/kmers objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/34/50d322f0e37b119842690ac80452a5fc686a00.debug debian/spaln/usr/bin/kmers install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/spaln objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ab/cae5f323398b73002b9bcc0214cb0cfe30d511.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/dvn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/dvn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/e5/ea39d23dc4e5fac196424f8754987784c46e51.debug debian/spaln/usr/bin/dvn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/fitild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/fitild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/07/0ac648f6f60726285b78e733193505dd0ac3ef.debug debian/spaln/usr/bin/fitild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/compild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/compild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/95/b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4.debug debian/spaln/usr/bin/compild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/exinpot debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/exinpot objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/55/86fef186af78965ee257b0bcb5cc4a7fba9d17.debug debian/spaln/usr/bin/exinpot install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/utn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/utn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9c/08c35d4a3b17f4727b2956ebef81c3a87d5671.debug debian/spaln/usr/bin/utn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/plotild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/plotild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/68/9dcc00122bec624cd104a5450a08d5001b9e88.debug debian/spaln/usr/bin/plotild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/makmdm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/13/48c45ca8995d1c30fb7c902c327329b4578b21.debug debian/spaln/usr/bin/makmdm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/decompild debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/decompild objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/1c/e3b7e2ae0fd8793b7e04ad05cbd62cc0493655.debug debian/spaln/usr/bin/decompild install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/rdn debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/rdn objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/3c/3303bdc3af07eadabde6033d11f099593bcbe3.debug debian/spaln/usr/bin/rdn install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/sortgrcd objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/ca/6bbb6041eee4fbdb193cf3d029c858c673c998.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/npssm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug strip --remove-section=.comment --remove-section=.note debian/spaln/usr/bin/npssm objcopy --add-gnu-debuglink debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/66/313a39ff6d3953891b4569bcbd17851e765868.debug debian/spaln/usr/bin/npssm install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/spaln/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/spaln/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/spaln/usr/lib/debug install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/share/doc ln -s spaln debian/.debhelper/spaln/dbgsym-root/usr/share/doc/spaln-dbgsym install -m0755 -d debian/.debhelper/spaln dh_makeshlibs -a -O--sourcedirectory=src rm -f debian/spaln/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN dpkg-shlibdeps -Tdebian/spaln.substvars debian/spaln/usr/bin/makdbs debian/spaln/usr/bin/kmers debian/spaln/usr/bin/spaln debian/spaln/usr/bin/dvn debian/spaln/usr/bin/fitild debian/spaln/usr/bin/compild debian/spaln/usr/bin/exinpot debian/spaln/usr/bin/utn debian/spaln/usr/bin/plotild debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/decompild debian/spaln/usr/bin/rdn debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/npssm dh_installdeb -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN install -m0755 -d debian/spaln-data/DEBIAN dh_gencontrol -O--sourcedirectory=src install -m0755 -d debian/spaln/DEBIAN echo misc:Depends= >> debian/spaln.substvars echo misc:Pre-Depends= >> debian/spaln.substvars install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=070ac648f6f60726285b78e733193505dd0ac3ef 1348c45ca8995d1c30fb7c902c327329b4578b21 1ce3b7e2ae0fd8793b7e04ad05cbd62cc0493655 3450d322f0e37b119842690ac80452a5fc686a00 3c3303bdc3af07eadabde6033d11f099593bcbe3 5586fef186af78965ee257b0bcb5cc4a7fba9d17 66313a39ff6d3953891b4569bcbd17851e765868 689dcc00122bec624cd104a5450a08d5001b9e88 95b4a88b3eda60e8feba8f2dbc8e100ac9abdfe4 9c08c35d4a3b17f4727b2956ebef81c3a87d5671 abcae5f323398b73002b9bcc0214cb0cfe30d511 ca6bbb6041eee4fbdb193cf3d029c858c673c998 e5ea39d23dc4e5fac196424f8754987784c46e51 ea32f5007eff9fb98ed92ce0436ed02987f56e74" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/spaln-data/DEBIAN echo misc:Depends= >> debian/spaln-data.substvars echo misc:Pre-Depends= >> debian/spaln-data.substvars dpkg-gencontrol -pspaln-data -ldebian/changelog -Tdebian/spaln-data.substvars -cdebian/control -Pdebian/spaln-data chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/control dpkg-gencontrol -pspaln -ldebian/changelog -Tdebian/spaln.substvars -cdebian/control -Pdebian/spaln dpkg-gencontrol: warning: package spaln-data: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/spaln-data/DEBIAN/control chmod 0644 -- debian/spaln/DEBIAN/control dh_md5sums -O--sourcedirectory=src install -m0755 -d debian/spaln-data/DEBIAN install -m0755 -d debian/spaln/DEBIAN cd debian/spaln >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/spaln-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/spaln/DEBIAN/md5sums install -m0755 -d debian/.debhelper/spaln/dbgsym-root/DEBIAN cd debian/.debhelper/spaln/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/spaln-data/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src dpkg-deb --root-owner-group --build debian/spaln .. dpkg-deb --root-owner-group --build debian/.debhelper/spaln/dbgsym-root .. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln' in '../spaln_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-dbgsym' in '../spaln-dbgsym_3.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_3.0.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_3.0.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_3.0.2+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3474203 and its subdirectories I: Current time: Mon Feb 9 16:26:42 -12 2026 I: pbuilder-time-stamp: 1770697602 12,13c12,13 < bsdextrautils (= 2.40.2-13), < bsdutils (= 1:2.40.2-13), --- > bsdextrautils (= 2.40.2-14), > bsdutils (= 1:2.40.2-14), 58c58 < libblkid1 (= 2.40.2-13), --- > libblkid1 (= 2.40.2-14), 97c97 < libmount1 (= 2.40.2-13), --- > libmount1 (= 2.40.2-14), 111c111 < libsmartcols1 (= 2.40.2-13), --- > libsmartcols1 (= 2.40.2-14), 123c123 < libuuid1 (= 2.40.2-13), --- > libuuid1 (= 2.40.2-14), 144c144 < util-linux (= 2.40.2-13), --- > util-linux (= 2.40.2-14), UPDATE 1 Tue Jan 7 22:03:43 UTC 2025 - https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_22/29926/console.log encountered a problem: different packages were installed in the 1st+2nd builds and also in the 2nd+3rd build. -rw-r--r-- 1 jenkins jenkins 5397 Jan 7 22:03 ./b1/spaln_3.0.2+dfsg-2_amd64.buildinfo on ionos5-amd64.debian.net -rw-r--r-- 1 jenkins jenkins 5386 Jan 7 22:01 ./b2/spaln_3.0.2+dfsg-2_amd64.buildinfo on ionos11-amd64.debian.net Starting cleanup. /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/rbuildlog.K7fv954: 83.7% -- replaced with /srv/reproducible-results/rbuild-debian/r-b-build.9qh6YiaX/rbuildlog.K7fv954.gz [2025-01-07 22:03:43] INFO: Starting at 2025-01-07 22:03:43.728292 [2025-01-07 22:03:43] INFO: Generating the pages of 1 package(s) [2025-01-07 22:03:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/spaln_3.0.2+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/spaln_3.0.2+dfsg-2.diff.gz is missing [2025-01-07 22:03:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/spaln_3.0.2+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/spaln_3.0.2+dfsg-2.diff.gz is missing [2025-01-07 22:03:44] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/spaln_3.0.2+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/spaln_3.0.2+dfsg-2.diff.gz is missing [2025-01-07 22:03:44] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/spaln_3.0.2+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/spaln_3.0.2+dfsg-2.diff.gz is missing [2025-01-07 22:03:44] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/spaln_2.4.13f+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/spaln_2.4.13f+dfsg-1.diff.gz is missing [2025-01-07 22:03:44] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/spaln_2.4.13f+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/spaln_2.4.13f+dfsg-1.diff.gz is missing [2025-01-07 22:03:44] INFO: Finished at 2025-01-07 22:03:44.103491, took: 0:00:00.375206 All cleanup done. Tue Jan 7 22:03:44 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-oZxOVGvl, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 12min 5.161s CPU time consumed: 6.197s