Sun Apr 23 02:09:12 UTC 2023 I: starting to build spaln/bookworm/amd64 on jenkins on '2023-04-23 02:08' Sun Apr 23 02:09:12 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_19/10347/console.log Sun Apr 23 02:09:12 UTC 2023 I: Downloading source for bookworm/spaln=2.4.13f+dfsg-1 --2023-04-23 02:09:12-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/spaln/spaln_2.4.13f%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2209 (2.2K) [text/prs.lines.tag] Saving to: ‘spaln_2.4.13f+dfsg-1.dsc’ 0K .. 100% 210M=0s 2023-04-23 02:09:12 (210 MB/s) - ‘spaln_2.4.13f+dfsg-1.dsc’ saved [2209/2209] Sun Apr 23 02:09:12 UTC 2023 I: spaln_2.4.13f+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: spaln Binary: spaln, spaln-data Architecture: amd64 arm64 mips64el ppc64el s390x alpha ia64 kfreebsd-amd64 ppc64 riscv64 sparc64 all Version: 2.4.13f+dfsg-1 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 Package-List: spaln deb science optional arch=amd64,arm64,mips64el,ppc64el,s390x,alpha,ia64,kfreebsd-amd64,ppc64,riscv64,sparc64 spaln-data deb science optional arch=all Checksums-Sha1: 72592af468ec7fc398781a1dfb1f24f2608d2267 19683708 spaln_2.4.13f+dfsg.orig.tar.xz 4a9d261024900d15608505bb8f4e3b175cfaaaa8 13668 spaln_2.4.13f+dfsg-1.debian.tar.xz Checksums-Sha256: 68fa7af1b32e9deee7a73d7e18a8772903f2668684c521cbed4201c509adeeb6 19683708 spaln_2.4.13f+dfsg.orig.tar.xz 8a06b3c82424874c50192392214a42144ebe55407bd94946b87fd5138b3d47e6 13668 spaln_2.4.13f+dfsg-1.debian.tar.xz Files: dbacf8e975b81adfbafa447436888436 19683708 spaln_2.4.13f+dfsg.orig.tar.xz 4fd531ebf9b66e95bdef1f809c8744b7 13668 spaln_2.4.13f+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPgGTYOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtGnkw/+MokLEuNACDshymfc7CaD0H+7nzN3D2fnQfmC gyy51wzULqGm8f3ST+162K4z5XhZt/kLZaOca0sg9LaXyf8ceKEftMw6lKI6AnCK 4RJm4vPfXELDB/EUJ/R5IhBxLO96fBZB1FtapSQKbeQefuovkL1qu9ZUHC0HPBzS e/h5J+ub+WVKegUz3e+rU1qapuBOWtiKFDRlSYguRmVrf5+0TdFffI8qhiDnRuat IOGklA3LXQN1R2q04UWgDNUPIQ9XABPL4gprnTMCEV/tndypjB9/H9aYV1MrX61s bW+WNrCstpvFmYmx8qluKyKVMhKyzZF54epe9dXDuwqzAXfPbW506PXkeJPOozj9 7ffFEuW9nOAX/HraGPaWOsef+iPB/yCdl+EaXFU+9ZxdqL3Wu0TPe4BTFvCAc+HX szsssJIGeyLWhvD3nMfhbyA/jBgrGJYVvkwuZmypsFpobEe3qh2edotHxl2ZUDLg iJa+7/BJdhfJ5Wy9aPZbN6HemIcFkrj21W40UDFdZ04tItA5GXnz9XpGBIen0JYg RF1MfOBhKMJC4TG9D+pfkhPPQ037xKqnSiAwsePAsCYasxpDCrJDhKNU+6DonMGh m1pXZCj+0MiUMhyyhxscHbeS5Co/ysuzPf8fAzKQ/t25o3+PwqP4GWwK2PYMYFoC Rt38WBw= =lSBs -----END PGP SIGNATURE----- Sun Apr 23 02:09:12 UTC 2023 I: Checking whether the package is not for us Sun Apr 23 02:09:13 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Apr 23 02:09:13 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Apr 23 02:13:04 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 22 14:09:15 -12 2023 I: pbuilder-time-stamp: 1682215755 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.4.13f+dfsg-1.dsc] I: copying [./spaln_2.4.13f+dfsg.orig.tar.xz] I: copying [./spaln_2.4.13f+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 5 09:01:42 2023 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./spaln_2.4.13f+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting spaln in spaln-2.4.13f+dfsg dpkg-source: info: unpacking spaln_2.4.13f+dfsg.orig.tar.xz dpkg-source: info: unpacking spaln_2.4.13f+dfsg-1.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/1987253/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='92aace7e704b4f62b0f78c318308078e' 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='1987253' 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.Xpz017W0/pbuilderrc_h8Q3 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/b1 --logfile b1/build.log spaln_2.4.13f+dfsg-1.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://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1987253/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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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. 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 73.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 19.6 MB in 0s (45.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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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/spaln-2.4.13f+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_2.4.13f+dfsg-1_source.changes dpkg-buildpackage: info: source package spaln dpkg-buildpackage: info: source version 2.4.13f+dfsg-1 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/spaln-2.4.13f+dfsg' dh_auto_clean || true rm -f src/dbs.h src/iolib.h src/*.o src/*.a src/Makefile make[1]: Leaving directory '/build/spaln-2.4.13f+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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) 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/spaln-2.4.13f+dfsg' # the configure script is not originated from autoconf and needs to be manually called cd src && AR="x86_64-linux-gnu-ar rc" ./configure --exec_prefix=/usr/bin OK, CXX=x86_64-linux-gnu-g++ CFLAGS=-g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -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/spaln-2.4.13f+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/spaln-2.4.13f+dfsg' dh_auto_build -- table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin cd src && make -j15 table_dir=/usr/share/spaln/table alndbs_dir=/usr/share/spaln/seqdb exec_prefix=/usr/bin make[2]: Entering directory '/build/spaln-2.4.13f+dfsg/src' x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c spaln.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c gaps.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c codepot.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c divseq.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c gsinfo.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2b1.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2d1.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2h1.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2s1.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c bitpat.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c eijunc.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c seq.cc seq.cc: In member function 'Seq* Seq::aliaseq(Seq*, const bool&)': seq.cc:411:15: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class Seq' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 411 | memcpy(dest, this, sizeof(Seq)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from seq.cc:23: seq.h:226:7: note: 'class Seq' declared here 226 | class Seq { | ^~~ seq.cc: In function 'void reportseq(Seq**, int)': seq.cc:482:50: warning: format '%p' expects argument of type 'void*', but argument 9 has type 'int*' [-Wformat=] 482 | printf("%d\t%d\t%d\t%d\t%d\t%d\t%p\t%p\n", i + 1, | ~^ | | | void* | %n 483 | sd->sid, sd->vrtl, sd->len, sd->area_, sd->did, sd->seq_, sd->lens); | ~~~~~~~~ | | | int* seq.cc: In member function 'CHAR* Seq::seq_realloc()': seq.cc:538:33: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 538 | } catch (std::bad_alloc ba) { | ^~ eijunc.cc: In member function 'EiJuncSeq::EiJuncSeq(Eijmode, char const*, char const*, int)': eijunc.cc:150:20: warning: 'strncpy' output may be truncated copying 8 bytes from a string of length 255 [-Wstringop-truncation] 150 | strncpy(genome, str, 8); | ^ eijunc.cc:154:16: warning: 'strncpy' output may be truncated copying 8 bytes from a string of length 255 [-Wstringop-truncation] 154 | strncpy(genspc, genome, 8); | ^ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c simmtx.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c sqpr.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c utilseq.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c vmf.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c wln.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c boyer_moore.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c clib.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c iolib.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c mfile.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c sets.cc x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c supprime.cc 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 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -o makmdm makmdm.cc clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now makmdm.cc: In function 'void exp_qdt(double (*)[20], double*, double, int)': makmdm.cc:395:15: warning: unused variable 'q' [-Wunused-variable] 395 | static double q[2][20][20] = { | ^ makmdm.cc: At global scope: makmdm.cc:395:15: warning: 'q' defined but not used [-Wunused-variable] 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 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -o spaln spaln.o 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 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=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 -ffile-prefix-map=/build/spaln-2.4.13f+dfsg=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -pedantic -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -o makdbs makdbs.cc sblib.a clib.a -lpthread -lm -lz -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now sortgrcd.cc: In function 'int count_record(const char*, const char*, size_t)': sortgrcd.cc:997:25: warning: ISO C++ forbids variable length array 'buf' [-Wvla] 997 | char buf[rcdsize]; | ^~~ spaln.cc: In function 'blkaln.constprop': spaln.cc:801:46: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 801 | Gsinfo* GsI = new Gsinfo[nparalog + 1]; | ^ /usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/build/spaln-2.4.13f+dfsg/src' make[1]: Leaving directory '/build/spaln-2.4.13f+dfsg' dh_auto_test -O--sourcedirectory=src cd src && make -j15 test "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/spaln-2.4.13f+dfsg/src' please make install before test make[1]: Leaving directory '/build/spaln-2.4.13f+dfsg/src' rm -fr -- /tmp/dh-xdg-rundir-KeZKQHs5 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/spaln-2.4.13f+dfsg' dh_auto_install -- table_dir=/build/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/table alndbs_dir=/build/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/seqdb exec_prefix=/build/spaln-2.4.13f+dfsg/debian/spaln//usr/bin install -m0755 -d /build/spaln-2.4.13f\+dfsg/debian/tmp cd src && make -j15 install DESTDIR=/build/spaln-2.4.13f\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no table_dir=/build/spaln-2.4.13f\+dfsg/debian/spaln-data//usr/share/spaln/table alndbs_dir=/build/spaln-2.4.13f\+dfsg/debian/spaln-data//usr/share/spaln/seqdb exec_prefix=/build/spaln-2.4.13f\+dfsg/debian/spaln//usr/bin make[2]: Entering directory '/build/spaln-2.4.13f+dfsg/src' test -d /build/spaln-2.4.13f+dfsg/debian/spaln//usr/bin || mkdir -p /build/spaln-2.4.13f+dfsg/debian/spaln//usr/bin cp spaln sortgrcd makmdm makdbs /build/spaln-2.4.13f+dfsg/debian/spaln//usr/bin test -d /build/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/table || mkdir -p /build/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/table ./makmdm /build/spaln-2.4.13f+dfsg/debian/spaln-data//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/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/seqdb || mkdir -p /build/spaln-2.4.13f+dfsg/debian/spaln-data//usr/share/spaln/seqdb make[2]: Leaving directory '/build/spaln-2.4.13f+dfsg/src' make[1]: Leaving directory '/build/spaln-2.4.13f+dfsg' dh_install -O--sourcedirectory=src 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/sortgrcd.1.dh-new debian/spaln/usr/share/man/man1/sortgrcd.1 chmod 0644 -- 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 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 1675629762 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 gzip -9nf 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/README.md usr/share/doc/spaln/changelog.Debian usr/share/man/man1/sortgrcd.1 usr/share/man/man1/spaln.1 cd '/build/spaln-2.4.13f+dfsg' cd '/build/spaln-2.4.13f+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-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/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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-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 -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/makdbs debian/spaln/usr/bin/makmdm debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/spaln 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/6f objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/spaln debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/6f/b4b92de42161e6c12737023a47a007caf41827.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/6f/b4b92de42161e6c12737023a47a007caf41827.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/6f/b4b92de42161e6c12737023a47a007caf41827.debug debian/spaln/usr/bin/spaln install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a5 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/sortgrcd debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a5/a09dab95067bafc476c53fa901c69c4c9553f0.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a5/a09dab95067bafc476c53fa901c69c4c9553f0.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/a5/a09dab95067bafc476c53fa901c69c4c9553f0.debug debian/spaln/usr/bin/sortgrcd install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makdbs debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9e/0fb8bd880dacbaf657130c584ab71a92526ffd.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/9e/0fb8bd880dacbaf657130c584ab71a92526ffd.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/9e/0fb8bd880dacbaf657130c584ab71a92526ffd.debug debian/spaln/usr/bin/makdbs install -m0755 -d debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a8 objcopy --only-keep-debug --compress-debug-sections debian/spaln/usr/bin/makmdm debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a8/2f62019602197e27a7577ce5a4d8bf54c6358b.debug chmod 0644 -- debian/.debhelper/spaln/dbgsym-root/usr/lib/debug/.build-id/a8/2f62019602197e27a7577ce5a4d8bf54c6358b.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/a8/2f62019602197e27a7577ce5a4d8bf54c6358b.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/spaln debian/spaln/usr/bin/sortgrcd debian/spaln/usr/bin/makdbs 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-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 -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 -Pdebian/.debhelper/spaln/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=spaln-dbgsym "-DDepends=spaln (= \${binary:Version})" "-DDescription=debug symbols for spaln" "-DBuild-Ids=6fb4b92de42161e6c12737023a47a007caf41827 9e0fb8bd880dacbaf657130c584ab71a92526ffd a5a09dab95067bafc476c53fa901c69c4c9553f0 a82f62019602197e27a7577ce5a4d8bf54c6358b" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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 -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: building package 'spaln-dbgsym' in '../spaln-dbgsym_2.4.13f+dfsg-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/spaln-data .. dpkg-deb: building package 'spaln' in '../spaln_2.4.13f+dfsg-1_amd64.deb'. dpkg-deb: building package 'spaln-data' in '../spaln-data_2.4.13f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../spaln_2.4.13f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../spaln_2.4.13f+dfsg-1_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: including full 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/1987253 and its subdirectories I: Current time: Sat Apr 22 14:13:03 -12 2023 I: pbuilder-time-stamp: 1682215983 Sun Apr 23 02:13:04 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Apr 23 02:13:04 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Apr 23 02:15:02 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Apr 23 02:15:03 UTC 2023 I: spaln_2.4.13f+dfsg-1_amd64.changes: Format: 1.8 Date: Sun, 05 Feb 2023 21:42:42 +0100 Source: spaln Binary: spaln spaln-data spaln-dbgsym Architecture: all amd64 Version: 2.4.13f+dfsg-1 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) Changes: spaln (2.4.13f+dfsg-1) unstable; urgency=medium . * Team upload. * Ignore i386 in Salsa CI * Add CPPFLAGS for hardening Checksums-Sha1: efa3eddac4e0b689f6c321191c765a662fddeca6 19480552 spaln-data_2.4.13f+dfsg-1_all.deb f06711306ab8564f28ab7a63465db79cdd2d0a64 1558304 spaln-dbgsym_2.4.13f+dfsg-1_amd64.deb a48dda7af0b7ce6dc8bbe8328820226d478eabfb 5447 spaln_2.4.13f+dfsg-1_amd64.buildinfo f43a0a71d4335d25f99705b4ac04a672bba149b6 346852 spaln_2.4.13f+dfsg-1_amd64.deb Checksums-Sha256: 8edeeef73354e656582b81b1d93e6d20e551e770784a0773656132cab9eb6396 19480552 spaln-data_2.4.13f+dfsg-1_all.deb fc9868589da789717d03a33e5c6e68709366264630bbef33e6c83079583d39ea 1558304 spaln-dbgsym_2.4.13f+dfsg-1_amd64.deb 33d5b9575abb703643d9414684ad6622837cdc8ca8fe4da7bac5b275d86a9a89 5447 spaln_2.4.13f+dfsg-1_amd64.buildinfo 2d77380b0ea3a3c4c4fca041b49e6cd784ae469e1e38bb99d09f1dcd63c9ae7b 346852 spaln_2.4.13f+dfsg-1_amd64.deb Files: a214ea97ac5b4b3131b03a14952033d9 19480552 science optional spaln-data_2.4.13f+dfsg-1_all.deb 28efa22dd203c99e2adce0ef7a8c0ecc 1558304 debug optional spaln-dbgsym_2.4.13f+dfsg-1_amd64.deb 9d49ff2cf0cc1cfd7ae0a27ce63579cc 5447 science optional spaln_2.4.13f+dfsg-1_amd64.buildinfo 8b5b8dbd677c6163937368eebcb797b6 346852 science optional spaln_2.4.13f+dfsg-1_amd64.deb Sun Apr 23 02:15:04 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/spaln_2.4.13f+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/spaln_2.4.13f+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/spaln_2.4.13f+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/b1/spaln_2.4.13f+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Xpz017W0/b2/spaln_2.4.13f+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.727s) 0.727s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.291s) 0.290s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sun Apr 23 02:15:06 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 23 02:15:06 UTC 2023 I: spaln from bookworm built successfully and reproducibly on amd64. Sun Apr 23 02:15:07 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Apr 23 02:15:07 UTC 2023 I: Submitting 8.0K b1/spaln_2.4.13f+dfsg-1_amd64.buildinfo.asc Sun Apr 23 02:15:08 UTC 2023 I: Submitting 8.0K b2/spaln_2.4.13f+dfsg-1_amd64.buildinfo.asc Sun Apr 23 02:15:08 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 23 02:15:08 UTC 2023 I: Done submitting .buildinfo files. Sun Apr 23 02:15:08 UTC 2023 I: Removing signed spaln_2.4.13f+dfsg-1_amd64.buildinfo.asc files: removed './b1/spaln_2.4.13f+dfsg-1_amd64.buildinfo.asc' removed './b2/spaln_2.4.13f+dfsg-1_amd64.buildinfo.asc'