Tue Aug 10 09:00:59 UTC 2021 I: starting to build kalign/bullseye/arm64 on jenkins on '2021-08-10 09:00' Tue Aug 10 09:00:59 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/26481/console.log Tue Aug 10 09:00:59 UTC 2021 I: Downloading source for bullseye/kalign=1:3.3-1 --2021-08-10 09:01:00-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kalign/kalign_3.3-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1941 (1.9K) Saving to: ‘kalign_3.3-1.dsc’ 0K . 100% 194M=0s 2021-08-10 09:01:00 (194 MB/s) - ‘kalign_3.3-1.dsc’ saved [1941/1941] Tue Aug 10 09:01:00 UTC 2021 I: kalign_3.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kalign Binary: kalign Architecture: any Version: 1:3.3-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://msa.sbc.su.se/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kalign Vcs-Git: https://salsa.debian.org/med-team/kalign.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsimde-dev Package-List: kalign deb science optional arch=any Checksums-Sha1: f1f270aabed1ec034e9b34beb4eb683bd3d25c51 940232 kalign_3.3.orig.tar.gz fb872a4011d95bea9d8d9c7e38d1321fc8848775 14048 kalign_3.3-1.debian.tar.xz Checksums-Sha256: bb49b531ad320881154976194acb8cc0c519715b0d422eac7a171cc246f88d59 940232 kalign_3.3.orig.tar.gz 10c07e8fd2ea72d3e5426b228164834eed87d327b2c1fbb2ff910120372c8476 14048 kalign_3.3-1.debian.tar.xz Files: f160bffa437f8a5f13eb66ea100883bd 940232 kalign_3.3.orig.tar.gz 10caf1590fe5fdf47ab8170bf0462bac 14048 kalign_3.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl+lGh0ACgkQPCZ2P2xn 5uL7pBAApxfNaf7prTNWGh2vvfGs8Wdg4Gf00TRVdvikVGYtCx3rgY6zqD1dTmzx ezk9XCY3RZzZmp1Vc9dTW6wTbfL0hUs+QWywz7sXKU2IGyoyYeijhhTXwkSJcTaD VxwDFjdKYE98LZbUu9SoddsFrt+T9+eQSQ05AthC8hYdGtQQzD0OD0APx5R0vrld EjZ48mNUNYtvvlKm0kqegNK3CYchQxzn0CR8vzldc9RDnxAu2Q9dWZY7wnSQxjbz O+7Wg1joZTo4Ejgj/7e1S52gO9VNvHt6zCnARy8R3j9AxeQsSYx5Zg1qpjT4m2of Rj5EPlYSowYu/S5sRXN70JoXrWS4hync9h45aEM0XTiPbpOZKkn4BTPL6Cp+EuqW 06iFDZGrl1tP85h9zhKMJCDnkclLL3AmTI053u87q1FvPpqV82FlX6ttNVvaQOdm vAgbyBQXaFQiLY+32NiFrN940o6ZDz3/DoGlz5nImuKJdKlY1ot6UoJFHACyRJNh ebRxob9+rPZTBXBj3r64NKu4ofRf9D21vv+2W6MiSbHimiRetvFmqNQLocPCSvew NzpNQIs+85KruQ9NblcKyMSHWDgIdPwehA0Ii5JWuOMWwCb9dngjxAvpYxLIIeKa vpELFHr1BncN5VKzxbmxPc+3Zvfd+DfCSO6rM5pJBsUd9P4NUzI= =Eh2o -----END PGP SIGNATURE----- Tue Aug 10 09:01:00 UTC 2021 I: Checking whether the package is not for us Tue Aug 10 09:01:00 UTC 2021 I: Starting 1st build on remote node codethink10-arm64.debian.net. Tue Aug 10 09:01:00 UTC 2021 I: Preparing to do remote build '1' on codethink10-arm64.debian.net. Tue Aug 10 09:02:26 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 9 21:01:02 -12 2021 I: pbuilder-time-stamp: 1628586062 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [kalign_3.3-1.dsc] I: copying [./kalign_3.3.orig.tar.gz] I: copying [./kalign_3.3-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.xOoMOluz/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 5 21:40:45 2020 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kalign_3.3-1.dsc dpkg-source: info: extracting kalign in kalign-3.3 dpkg-source: info: unpacking kalign_3.3.orig.tar.gz dpkg-source: info: unpacking kalign_3.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying simde dpkg-source: info: applying no-native-build dpkg-source: info: applying keep-debugging I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8697/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='8697' 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/tmp.iioITt4Gql/pbuilderrc_bfND --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/b1 --logfile b1/build.log kalign_3.3-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink10-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 8 23:21 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/8697/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsimde-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 ... 19646 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 libsimde-dev; however: Package libsimde-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} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 18.2 MB of archives. After unpacking 71.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libsimde-dev all 0.7.2-4 [259 kB] Fetched 18.2 MB in 3s (5409 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../10-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../23-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../25-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/kalign-3.3/ && 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 > ../kalign_3.3-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT' configure.ac:5: installing './compile' configure.ac:16: installing './config.guess' configure.ac:16: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for gawk... 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(cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder1 configure: Host system: aarch64-unknown-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- debian/rules override_dh_auto_build make[1]: Entering directory '/build/kalign-3.3' dh_auto_build make -j8 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[1]: Leaving directory '/build/kalign-3.3' dh_auto_test make -j8 check VERBOSE=1 make[1]: Entering directory '/build/kalign-3.3' Making check in src make[2]: Entering directory '/build/kalign-3.3/src' make edist alphabet misc_test bpm_test rwaln rstdin_test make[3]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-euclidean_dist.o `test -f 'euclidean_dist.c' || echo './'`euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-misc.o `test -f 'misc.c' || echo './'`misc.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-bpm.o `test -f 'bpm.c' || echo './'`bpm.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-tlmisc.o `test -f 'tlmisc.c' || echo './'`tlmisc.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-rwalign.o `test -f 'rwalign.c' || echo './'`rwalign.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o read_from_stdin_test.o read_from_stdin_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm -fopenmp make[3]: Leaving directory '/build/kalign-3.3/src' make check-TESTS make[3]: Entering directory '/build/kalign-3.3/src' make[4]: Entering directory '/build/kalign-3.3/src' PASS: misc_test PASS: alphabet PASS: rstdin_test PASS: edist PASS: bpm_test ============================================================================ Testsuite summary for kalign 3.3 ============================================================================ # TOTAL: 5 # PASS: 5 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' make[2]: Leaving directory '/build/kalign-3.3/src' Making check in dev make[2]: Entering directory '/build/kalign-3.3/dev' make check-TESTS make[3]: Entering directory '/build/kalign-3.3/dev' Running kalign basic io test: a2m.good.1 read/writea2m.good.1 SUCCESS a2m.good.2 read/writea2m.good.2 SUCCESS afa.good.1 read/writeafa.good.1 SUCCESS afa.good.2 read/writeafa.good.2 SUCCESS afa.good.3 read/writeafa.good.3 SUCCESS clustal.good.1 read/writeclustal.good.1 SUCCESS clustal.good.2 read/writeclustal.good.2 SUCCESS PASS: run_io_test.sh Running kalign basic alignment tests: BB11001.msf read/writeBB11001.msf SUCCESS BB11001_EOF.msf read/writeBB11001_EOF.msf SUCCESS BB11001.tfa read/writeBB11001.tfa SUCCESS BB12006.msf read/writeBB12006.msf SUCCESS BB12006.tfa read/writeBB12006.tfa SUCCESS BB30014.msf read/writeBB30014.msf SUCCESS BB30014.tfa read/writeBB30014.tfa SUCCESS PASS: run_aln_test.sh ================== All 2 tests passed ================== make[3]: Leaving directory '/build/kalign-3.3/dev' make[2]: Leaving directory '/build/kalign-3.3/dev' make[2]: Entering directory '/build/kalign-3.3' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/kalign-3.3' make[1]: Leaving directory '/build/kalign-3.3' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/kalign-3.3' dh_auto_install make -j1 install DESTDIR=/build/kalign-3.3/debian/kalign AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/kalign-3.3' Making install in src make[3]: Entering directory '/build/kalign-3.3/src' make[4]: Entering directory '/build/kalign-3.3/src' /bin/mkdir -p '/build/kalign-3.3/debian/kalign/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c kalign kchaos '/build/kalign-3.3/debian/kalign/usr/bin' libtool: install: /usr/bin/install -c kalign /build/kalign-3.3/debian/kalign/usr/bin/kalign libtool: install: /usr/bin/install -c kchaos /build/kalign-3.3/debian/kalign/usr/bin/kchaos make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making install in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[4]: Entering directory '/build/kalign-3.3/dev' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/kalign-3.3/dev' make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[4]: Entering directory '/build/kalign-3.3' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/kalign-3.3' make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[1]: Leaving directory '/build/kalign-3.3' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/kalign/usr/bin/kalign: DWARF compression not beneficial - old size 159862 new size 160226 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/kalign-3.3' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/kalign-3.3' dh_md5sums dh_builddeb dpkg-deb: building package 'kalign' in '../kalign_3.3-1_arm64.deb'. dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../kalign_3.3-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/8697 and its subdirectories I: Current time: Mon Aug 9 21:02:25 -12 2021 I: pbuilder-time-stamp: 1628586145 Tue Aug 10 09:02:27 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Tue Aug 10 09:02:27 UTC 2021 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Tue Aug 10 09:04:54 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Tue Aug 10 09:04:55 UTC 2021 I: kalign_3.3-1_arm64.changes: Format: 1.8 Date: Fri, 06 Nov 2020 10:40:38 +0100 Source: kalign Binary: kalign kalign-dbgsym Architecture: arm64 Version: 1:3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: kalign - Global and progressive multiple sequence alignment Changes: kalign (1:3.3-1) unstable; urgency=medium . * Team upload. * debian/watch: fix syntax * refresh patches; drop "hardening", it was applied upstream. * Added a patch to retain debugging symbols Checksums-Sha1: 5097d5f606b86108a57218398742c9ffde0cd18b 189812 kalign-dbgsym_3.3-1_arm64.deb 426d4c74ad3ba9d8a59f688b1cdcc06bb6f0bbed 4824 kalign_3.3-1_arm64.buildinfo 0954eb11d8cca4c5e09c615e4d982242d5448a70 73664 kalign_3.3-1_arm64.deb Checksums-Sha256: bf92df8205baed0439a58fbdf23bea5236ccafb0cb235f6063dccd6516ee077f 189812 kalign-dbgsym_3.3-1_arm64.deb 8b5abfa34a7bdf47a6868ad44f0b53dedd95a3f038052611ab7418d2d4fef2d5 4824 kalign_3.3-1_arm64.buildinfo 64f7614a01a80c3eea3cbfa387d06765b03b24b4cab3d8e7fcf3ebc0d746f01f 73664 kalign_3.3-1_arm64.deb Files: 7afb381119dd66794a73fb62602e8bf0 189812 debug optional kalign-dbgsym_3.3-1_arm64.deb d79f4cd4f6928f657f9b2721fd5b7962 4824 science optional kalign_3.3-1_arm64.buildinfo 45eba2ed34f29309832221838e4b2e9e 73664 science optional kalign_3.3-1_arm64.deb Tue Aug 10 09:04:56 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/kalign_3.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/kalign_3.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/kalign_3.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/b1/kalign_3.3-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.iioITt4Gql/b2/kalign_3.3-1_arm64.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: 0.227s) 0.227s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Aug 10 09:04:58 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Aug 10 09:04:58 UTC 2021 I: kalign from bullseye built successfully and reproducibly on arm64. Tue Aug 10 09:04:59 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Aug 10 09:04:59 UTC 2021 I: Submitting 8.0K b1/kalign_3.3-1_arm64.buildinfo.asc Tue Aug 10 09:05:00 UTC 2021 I: Submitting 8.0K b2/kalign_3.3-1_arm64.buildinfo.asc Tue Aug 10 09:05:01 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Aug 10 09:05:01 UTC 2021 I: Done submitting .buildinfo files. Tue Aug 10 09:05:01 UTC 2021 I: Removing signed kalign_3.3-1_arm64.buildinfo.asc files: removed './b1/kalign_3.3-1_arm64.buildinfo.asc' removed './b2/kalign_3.3-1_arm64.buildinfo.asc'