Fri Apr 28 12:25:45 UTC 2023 I: starting to build kalign/bookworm/arm64 on jenkins on '2023-04-28 12:25' Fri Apr 28 12:25:45 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_13/28509/console.log Fri Apr 28 12:25:45 UTC 2023 I: Downloading source for bookworm/kalign=1:3.3.5-1 --2023-04-28 12:25:45-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kalign/kalign_3.3.5-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1987 (1.9K) [text/prs.lines.tag] Saving to: ‘kalign_3.3.5-1.dsc’ 0K . 100% 124M=0s 2023-04-28 12:25:45 (124 MB/s) - ‘kalign_3.3.5-1.dsc’ saved [1987/1987] Fri Apr 28 12:25:45 UTC 2023 I: kalign_3.3.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kalign Binary: kalign Architecture: any Version: 1:3.3.5-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://msa.sbc.su.se/ Standards-Version: 4.6.2 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, cmake Package-List: kalign deb science optional arch=any Checksums-Sha1: 3fea52d0adba10c234f22d67a30cfa092b1aa012 901060 kalign_3.3.5.orig.tar.gz c2ec9a31d6871a73282a5b2a6cef326215c4780f 12092 kalign_3.3.5-1.debian.tar.xz Checksums-Sha256: 75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212 901060 kalign_3.3.5.orig.tar.gz 7bd9408e8f9f4607a2bf90f32ab9e369c23d68faae90d39de78b365b9d94cc74 12092 kalign_3.3.5-1.debian.tar.xz Files: 4634d95e88ea3bacfbad856afab91685 901060 kalign_3.3.5.orig.tar.gz 37078d0d0c95b24eb21f913597dfd214 12092 kalign_3.3.5-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPgoiURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEe4hAAm63IK4nPkJW2eB3uPZ7ElmR2zC5Fuw0W tFT4KlqCGrp/NZSfdq+BUW+OQJb36ErpEtzDTAST4Jg3W81bsYD7I4TIhIuOtsil qtXa0ku3UscMixoUyZ1jjueG0EkYhkfyWpXPL5XumvnxDnJtVPG+x35GHXKf3ahK 0nQ24KHEEAOMNbT+2/wddPxjkcOoWSSk5Q/oo8JyY8fhJTILjHXqYojuA48OuY32 aaUSccWXcwKl6656jdWh2OSH00VqHOAvAtVTUWkTG0Oa+GXpiiBtWb1WEKQLfGmR My0WuieoO9oAQw0lCSrkpbr0WyP8YF+WM99FhX7cW5M7oK7zCgHZlKpvkzoqfqfV JhJbHqI9c69tgo5BNL5jev0ZXmBCNtZSUtHeVElj/7tHwNsfinjaEbIUdRQuY8pH HRzIMjkXjSvt22PKSZCZfkoiDtYza2e1OhrTmp27AwmxfzVUc9ZhdOCA3j6Uuug3 46CvwuqaVOugyKRoCiMfmYhXXvp32LLs8V6LSqXHBbdqvdcX5V+lSvuUBMrtLqQj GYpV6J1o0dNSx2Dlz91a/x6Q8TTs3ZzoCB7WiN4YGekCc3ERRYrPTfweDw4ujCgi blBPnEmwTOI483DUsw8ZYsBPxEZXDq0/426+x//CTQFLv2uIeFqod0NVkPElxVqm vdQzoNJQp4g= =gBfm -----END PGP SIGNATURE----- Fri Apr 28 12:25:45 UTC 2023 I: Checking whether the package is not for us Fri Apr 28 12:25:45 UTC 2023 I: Starting 1st build on remote node codethink12-arm64.debian.net. Fri Apr 28 12:25:45 UTC 2023 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Fri Apr 28 12:26:57 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 28 00:25:48 -12 2023 I: pbuilder-time-stamp: 1682684748 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 [kalign_3.3.5-1.dsc] I: copying [./kalign_3.3.5.orig.tar.gz] I: copying [./kalign_3.3.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 5 18:45:57 2023 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kalign_3.3.5-1.dsc: no acceptable signature found dpkg-source: info: extracting kalign in kalign-3.3.5 dpkg-source: info: unpacking kalign_3.3.5.orig.tar.gz dpkg-source: info: unpacking kalign_3.3.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pass-proper-flags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10190/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 parallel=8' DISTRIBUTION='bookworm' 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='10190' 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.NIWpP6so/pbuilderrc_QenP --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.NIWpP6so/b1 --logfile b1/build.log kalign_3.3.5-1.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 codethink12-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 26 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/10190/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, cmake dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake 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} cmake{a} cmake-data{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} libarchive13{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 30.3 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-9 [362 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Fetched 30.3 MB in 1s (39.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../04-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-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 .../16-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../17-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../18-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../19-libarchive13_3.6.2-1_arm64.deb ... Unpacking libarchive13:arm64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../20-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../21-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../22-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../23-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../24-libnghttp2-14_1.52.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../25-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../26-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../27-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../28-libcurl4_7.88.1-9_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-9) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../29-libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../30-libjsoncpp25_1.9.5-4_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../31-librhash0_1.4.3-3_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../32-libuv1_1.44.2-1_arm64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/kalign-3.3.5/ && 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_3.3.5-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 debian/rules override_dh_auto_configure make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP is enabled. -- No SIMD level seems supported, building for baseline -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- -- Configuration: -- -------------------------------------- -- Build type : None -- Compiler flags : -- Compiler c debug flags : -g -- Compiler c release flags : -O3 -DNDEBUG -- Compiler c min size flags : -Os -DNDEBUG -- Compiler c flags : -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -MF CMakeFiles/tldevel.dir/src/tldevel.c.o.d -o CMakeFiles/tldevel.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_ALPHABET -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c [ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c [ 14%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c [ 15%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -MF CMakeFiles/bpm_utest.dir/src/alphabet.c.o.d -o CMakeFiles/bpm_utest.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c [ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -c /build/kalign-3.3.5/lib/src/tlmisc.c [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm.c.o -c /build/kalign-3.3.5/lib/src/bpm.c [ 20%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c [ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c [ 22%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/kalign-3.3.5/lib/src/tlmisc.c [ 24%] Linking C executable alphabet_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o /usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -MF CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c [ 27%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -MF CMakeFiles/task_utest.dir/src/tlrng.c.o.d -o CMakeFiles/task_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 28%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 28%] Built target alphabet_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm_test.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -c /build/kalign-3.3.5/lib/src/bpm_test.c [ 30%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/task_utest.dir/src/task.c.o -MF CMakeFiles/task_utest.dir/src/task.c.o.d -o CMakeFiles/task_utest.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c [ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/kalign-3.3.5/lib/src/msa_alloc.c [ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c [ 34%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -MF CMakeFiles/tldevel.dir/src/tlrng.c.o.d -o CMakeFiles/tldevel.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o /build/kalign-3.3.5/lib/src/task.c: In function 'read_tasks': /build/kalign-3.3.5/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 94 | fscanf( f_ptr, "%d", &n_tasks); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -c /build/kalign-3.3.5/lib/src/msa_op.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -c /build/kalign-3.3.5/lib/src/msa_io.c [ 38%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -c /build/kalign-3.3.5/lib/src/msa_misc.c [ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c [ 41%] Linking C executable task_utest [ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -c /build/kalign-3.3.5/lib/src/msa_check.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/task_utest.dir/src/tldevel.c.o CMakeFiles/task_utest.dir/src/tlrng.c.o CMakeFiles/task_utest.dir/src/task.c.o -o task_utest -lm [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/kalign-3.3.5/lib/src/msa_cmp.c make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 44%] Built target task_utest [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -MF CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c /build/kalign-3.3.5/lib/src/euclidean_dist.c: In function 'main': /build/kalign-3.3.5/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ [ 47%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -MF CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c [ 48%] Linking C executable bpm_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bpm_utest.dir/src/tldevel.c.o CMakeFiles/bpm_utest.dir/src/tlrng.c.o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o CMakeFiles/bpm_utest.dir/src/alphabet.c.o CMakeFiles/bpm_utest.dir/src/bpm.c.o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -o bpm_utest -lm [ 50%] Linking C executable edist_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/edist_utest.dir/src/tldevel.c.o CMakeFiles/edist_utest.dir/src/tlrng.c.o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -o edist_utest -lm make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 51%] Linking C static library libtldevel.a cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -MF CMakeFiles/kalign_OBJ.dir/src/task.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -c /build/kalign-3.3.5/lib/src/bisectingKmeans.c [ 54%] Built target bpm_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -MF CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -c /build/kalign-3.3.5/lib/src/sequence_distance.c [ 57%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 57%] Built target edist_utest cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bpm.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -c /build/kalign-3.3.5/lib/src/bpm.c /usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o /usr/bin/ranlib libtldevel.a make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -MF CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c [ 58%] Built target tldevel [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -c /build/kalign-3.3.5/lib/src/aln_wrap.c [ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -MF CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -c /build/kalign-3.3.5/lib/src/pick_anchor.c /build/kalign-3.3.5/lib/src/task.c: In function 'read_tasks': /build/kalign-3.3.5/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 94 | fscanf( f_ptr, "%d", &n_tasks); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -c /build/kalign-3.3.5/lib/src/aln_param.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -c /build/kalign-3.3.5/lib/src/aln_run.c [ 65%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/kalign-3.3.5/lib/src/aln_mem.c [ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/kalign-3.3.5/lib/src/aln_setup.c [ 68%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/kalign-3.3.5/lib/src/aln_controller.c [ 70%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/kalign-3.3.5/lib/src/aln_seqseq.c [ 71%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_seqprofile.c [ 72%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 74%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_profileprofile.c cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-aarch64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -MF CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/kalign-3.3.5/lib/src/weave_alignment.c make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 74%] Built target kalign_OBJ make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' cd /build/kalign-3.3.5/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-aarch64-linux-gnu /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' cd /build/kalign-3.3.5/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-aarch64-linux-gnu /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [ 77%] Linking C static library libkalign.a [ 77%] Linking C static library libkalign_static.a cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 /usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o 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/build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Built target kalign-bin [100%] Linking CXX executable kaligncpp cd /build/kalign-3.3.5/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic make[4]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' [100%] Built target kaligncpp make[3]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/kalign-3.3.5/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/kalign-3.3.5' debian/rules override_dh_auto_test make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_test cd obj-aarch64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 make[2]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j8 UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/kalign-3.3.5/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/kalign-3.3.5/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/kalign-3.3.5/obj-aarch64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: bpm_utest 1: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/bpm_utest 1: Working Directory: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib 1: Test timeout computed to be: 1500 test 2 Start 2: alphabet_utest 2: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/alphabet_utest 2: Working Directory: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib 2: Test timeout computed to be: 1500 test 3 Start 3: edist_utest 3: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/edist_utest 3: Working Directory: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib 3: Test timeout computed to be: 1500 test 4 Start 4: task_utest 4: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib/task_utest 4: Working Directory: /build/kalign-3.3.5/obj-aarch64-linux-gnu/lib 4: Test timeout computed to be: 1500 test 5 Start 5: C++Lib 5: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/tests/kaligncpp 5: Working Directory: /build/kalign-3.3.5/tests 5: Test timeout computed to be: 1500 test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB11001.tfa" 6: Working Directory: /build/kalign-3.3.5/tests 6: Test timeout computed to be: 1500 test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/kalign-3.3.5/tests 7: Test timeout computed to be: 1500 test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.msf" 8: Working Directory: /build/kalign-3.3.5/tests 8: Test timeout computed to be: 1500 1: LEN: 256 1: [2023-04-28 00:26:32] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 2: B 20 2: C 1 2: D 2 2: E 3 2: F 4 2: G 5 2: H 6 2: I 7 2: J -1 2: K 8 2: L 9 2: M 10 2: N 11 2: O -1 2: P 12 2: Q 13 2: R 14 2: S 15 2: T 16 2: U 20 2: V 17 2: W 18 2: X 20 2: Y 19 2: Z 20 2: [ -1 2: \ -1 2: ] -1 2: ^ -1 2: _ -1 2: LEN: 13 2: @ -1 2: A 0 2: B 2 2: C 1 2: D 2 2: E 3 2: F 4 2: G 5 2: H 6 2: I 7 2: J -1 2: K 8 2: L 9 2: M 9 2: N 2 2: O -1 2: P 10 2: Q 3 2: R 8 2: S 0 2: T 0 2: U -1 2: V 7 2: W 11 2: X 12 2: Y 4 2: Z 3 2: [ -1 2: \ -1 2: ] -1 2: ^ -1 2: _ -1 2: LEN: 5 2: @ -1 2: A 0 2: B 4 2: C 1 2: D 4 2: E -1 2: F -1 2: G 2 2: H 4 2: I -1 2: J -1 2: K 4 2: L -1 2: M 4 2: N 4 2: O -1 2: P -1 2: Q -1 2: R 4 2: S 4 2: T 3 2: U 3 2: V 4 2: W 4 2: X -1 2: Y 4 2: Z -1 2: [ -1 2: \ -1 2: ] -1 2: ^ -1 2: _ -1 2: LEN: 6 2: @ -1 2: A 0 2: B 5 2: C 1 2: D 2 2: E 2 2: F 1 2: G 3 2: H 3 2: I 1 2: J -1 2: K 2 2: L 4 2: M 0 2: N 2 2: O -1 2: P 2 2: Q 2 2: R 2 2: S 3 2: T 3 2: U -1 2: V 1 2: W 4 2: X 5 2: Y 4 2: Z 5 2: [ -1 2: \ -1 2: ] -1 2: ^ -1 2: _ -1 3: [2023-04-28 00:26:32] : LOG : Check for correctness. 3: [2023-04-28 00:26:32] : LOG : Timing serial 3: [2023-04-28 00:26:32] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 4: 770 796 165 864 576 4: 195 727 853 998 245 4: 964 11 177 958 866 4: 313 682 387 550 320 4: 273 624 850 798 115 4: 983 922 861 782 207 4: 425 855 945 232 968 4: 88 921 292 718 479 4: 753 73 54 186 238 4: 349 490 69 938 590 4: 141 958 730 154 127 4: 489 428 413 820 805 4: 621 824 461 901 407 4: 507 422 197 163 819 4: 244 305 991 265 369 4: 256 850 89 637 826 4: 520 188 45 768 398 4: 30 49 330 595 682 4: 696 189 873 68 660 4: 948 19 606 427 304 4: 846 750 546 753 743 4: 296 930 773 571 931 4: 924 963 545 66 677 4: 702 225 374 142 761 4: 761 424 475 667 748 4: 518 983 346 950 16 4: 61 715 951 961 490 4: 308 512 977 831 743 4: 454 51 859 60 640 4: 971 90 317 708 781 4: 805 253 796 110 302 4: 243 498 345 55 817 4: 416 182 855 794 54 4: 704 267 728 879 621 4: 744 651 213 447 717 4: 585 404 307 152 481 4: 601 137 761 387 175 4: 965 678 437 404 180 4: 62 910 238 524 234 4: 894 510 993 339 463 4: 48 257 636 965 764 4: 920 738 228 334 131 4: 744 3 360 785 554 4: 78 473 999 395 690 4: 831 253 969 216 127 4: 280 786 242 805 62 4: 355 700 428 522 77 4: 479 285 132 488 782 4: 653 655 314 108 133 4: 277 688 531 372 162 4: 502 932 78 83 293 4: 438 346 124 706 263 4: 308 802 13 677 396 4: 436 308 332 423 621 5: Aligned: 5: ------GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP---------- 5: ------------MQDRVKRPMNAFIVWSRDQRRKMAL-EN-PRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK---YPNYKYRP- 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS--N-L-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNA--- 5: ----------------MHIKKPLNAFMLYMKEMRANV-VA-ESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY 6: 6: Kalign (3.3.5) 6: 6: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 6: 6: This program comes with ABSOLUTELY NO WARRANTY; for details type: 6: `kalign -showw'. 6: This is free software, and you are welcome to redistribute it 6: under certain conditions; consult the COPYING file for details. 6: 6: Please cite: 6: Lassmann, Timo. 6: "Kalign 3: multiple sequence alignment of large data sets." 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: 6: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 6: [2023-04-28 00:26:32] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. 6: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 6: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2023-04-28 00:26:32] : LOG : Building guide tree. 6: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2023-04-28 00:26:32] : LOG : Aligning 6: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- 6: >1j46_A 6: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW 6: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 6: >1k99_A 6: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM 6: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 7: 7: Kalign (3.3.5) 7: 7: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 7: 7: This program comes with ABSOLUTELY NO WARRANTY; for details type: 7: `kalign -showw'. 7: This is free software, and you are welcome to redistribute it 7: under certain conditions; consult the COPYING file for details. 7: 7: Please cite: 7: Lassmann, Timo. 7: "Kalign 3: multiple sequence alignment of large data sets." 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: 7: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 7: [2023-04-28 00:26:32] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. 7: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 7: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2023-04-28 00:26:32] : LOG : Building guide tree. 7: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2023-04-28 00:26:32] : LOG : Aligning 7: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- 7: >1j46_A 7: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW 7: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 7: >1k99_A 7: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM 7: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 1/11 Test #2: alphabet_utest ................... Passed 0.03 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" 9: Working Directory: /build/kalign-3.3.5/tests 9: Test timeout computed to be: 1500 2/11 Test #3: edist_utest ...................... Passed 0.03 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" 10: Working Directory: /build/kalign-3.3.5/tests 10: Test timeout computed to be: 1500 3/11 Test #4: task_utest ....................... Passed 0.03 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/kalign-3.3.5/obj-aarch64-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB30014.tfa" 11: Working Directory: /build/kalign-3.3.5/tests 11: Test timeout computed to be: 1500 4/11 Test #5: C++Lib ........................... Passed 0.03 sec 5/11 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.03 sec 6/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.03 sec 8: 8: Kalign (3.3.5) 8: 8: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 8: 8: This program comes with ABSOLUTELY NO WARRANTY; for details type: 8: `kalign -showw'. 8: This is free software, and you are welcome to redistribute it 8: under certain conditions; consult the COPYING file for details. 8: 8: Please cite: 8: Lassmann, Timo. 8: "Kalign 3: multiple sequence alignment of large data sets." 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: 8: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 8: [2023-04-28 00:26:32] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. 8: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 8: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2023-04-28 00:26:32] : LOG : Building guide tree. 8: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2023-04-28 00:26:32] : LOG : Aligning 8: [2023-04-28 00:26:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF 8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ 8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ 8: KA--- 8: >1bbt_ac 8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- 8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF 8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY 8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- 8: ----- 8: >1bev_ac 8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N 8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC 8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG 8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ 8: TAILQ 8: >1mec_ac 8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- 8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF 8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 8: Q---- 9: 9: Kalign (3.3.5) 9: 9: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 9: 9: This program comes with ABSOLUTELY NO WARRANTY; for details type: 9: `kalign -showw'. 9: This is free software, and you are welcome to redistribute it 9: under certain conditions; consult the COPYING file for details. 9: 9: Please cite: 9: Lassmann, Timo. 9: "Kalign 3: multiple sequence alignment of large data sets." 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: 9: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 9: [2023-04-28 00:26:32] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. 9: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 10: 10: Kalign (3.3.5) 10: 10: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 10: 10: This program comes with ABSOLUTELY NO WARRANTY; for details type: 10: `kalign -showw'. 10: This is free software, and you are welcome to redistribute it 10: under certain conditions; consult the COPYING file for details. 10: 10: Please cite: 10: Lassmann, Timo. 10: "Kalign 3: multiple sequence alignment of large data sets." 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: 10: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 10: [2023-04-28 00:26:32] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. 10: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 7/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.03 sec 11: 11: Kalign (3.3.5) 11: 11: Copyright (C) 2006,2019,2020,2021 Timo Lassmann 11: 11: This program comes with ABSOLUTELY NO WARRANTY; for details type: 11: `kalign -showw'. 11: This is free software, and you are welcome to redistribute it 11: under certain conditions; consult the COPYING file for details. 11: 11: Please cite: 11: Lassmann, Timo. 11: "Kalign 3: multiple sequence alignment of large data sets." 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: 11: [2023-04-28 00:26:32] : LOG : Detected protein sequences. 11: [2023-04-28 00:26:32] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. 11: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2023-04-28 00:26:32] : LOG : Calculating pairwise distances 9: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2023-04-28 00:26:32] : LOG : Building guide tree. 9: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2023-04-28 00:26:32] : LOG : Aligning 11: [2023-04-28 00:26:32] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 11: [2023-04-28 00:26:32] : LOG : Building guide tree. 10: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2023-04-28 00:26:32] : LOG : Building guide tree. 10: [2023-04-28 00:26:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2023-04-28 00:26:32] : LOG : Aligning 9: [2023-04-28 00:26:32] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF 9: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ 9: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ 9: KA--- 9: >1bbt_ac 9: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- 9: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF 9: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY 9: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- 9: ----- 9: >1bev_ac 9: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N 9: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC 9: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG 9: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ 9: TAILQ 9: >1mec_ac 9: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- 9: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- 8/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.03 sec 10: [2023-04-28 00:26:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF 10: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ 10: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ 10: KA--- 10: >1bbt_ac 10: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- 10: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF 10: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY 10: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- 10: ----- 10: >1bev_ac 10: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N 10: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC 10: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG 10: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ 10: TAILQ 10: >1mec_ac 10: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- 10: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- 9/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.03 sec 11: [2023-04-28 00:26:32] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 11: [2023-04-28 00:26:32] : LOG : Aligning 11: [2023-04-28 00:26:32] : LOG : CPU Time: 0.11u 00:00:00.11 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- 11: SKYNLY-RKDIKEK--------ALIDMYIE-GIADLGEMILLLPFTQ------------- 11: -PEEQDAKLALIKEK-IKNRYFPAFEKVLKSH--GQDYL-VGNKLSRADIHLVELLYY-- 11: -----VEE--LDSSLIS--S-FPLLKALKTRI-SNLPTVKKFLQPGSPRKPPMDEKSLEE 11: ARKIFRF------- 11: >GTA1_BOVIN 11: ----------------------------------AGKPTLHYFNGRGRMECIRWLLAAAG 11: VEFEEKFIEKPEDLDKLKNDG--SLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- 11: TKYNLY-GKDMKER--------ALIDMYSE-GVADLGEMIMHFPLCP------------- 11: -PAEKDAKLTLIREK-TTNRYLPAFENVLKSH--GQDYL-VGNKLSRADIHLVELLYY-- 11: -----VEE--LDPSLLA--N-FPLLKALKARV-SSLPAVKKFLQPGSQRKPPTDEKKIEE 11: ARKVFKF------- 11: >GTA1_MOUSE 11: ----------------------------------AGKPVLHYFNARGRMECIRWLLAAAG 11: VEFEEKFIQSPEDLEKLKKDG--NLMFDQVPMVEI-----DG--MKLAQTRAILNYIA-- 11: TKYDLY-GKDMKER--------ALIDMYSE-GILDLTEMIGQLVLCP------------- 11: -PDQREAKTALAKDR-TKNRYLPAFEKVLKSH--GQDYL-VGNRLTRVDIHLLEVLLY-- 11: -----VEE--FDASLLT--P-FPLLKAFKSRI-SSLPNVKKFLQPGSQRKPPMDAKQIQE 11: ARKAFKIQ------ 11: >GTC1_RAT 11: ----------------------------------PGKPVLHYFDGRGRMEPIRWLLAAAG 11: VEFEEQFLKTRDDLARLRNDG--SLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- 11: TKYNLY-GKDMKER--------ALIDMYAE-GVADLDEIVLHYPYIP------------- 11: -PGEKEASLAKIKDK-ARNRYFPAFEKVLKSH--GQDYL-VGNRLSRADVYLVQVLYH-- 11: -----VEE--LDPSALA--N-FPLLKALRTRV-SNLPTVKKFLQPGSQRKPLEDEKCVES 11: AVKIFS-------- 11: >GTC_RABIT 11: ----------------------------------AGKPKLHYFNARGRMESIRWLLTAAG 11: VEFEEKCMKTREDLEKLRKDG--VLMFQQVPMVEI-----DG--MKLVQTRAIFNYIA-- 11: DKHNLY-GKDIKER--------ALIDMYTE-GIVDLNELILTRPFLP------------- 11: -PEEQEAKLAQIKDK-AKNRYFPAFEKVLKSH--GQDYL-VGNKLSKADILLVELLYN-- 11: -----VEE--LNPGATA--S-FPLLQALKTRI-SNLPTVKKFLQPGSQRNPPDDEKCREE 11: AKIIFH-------- 11: >GTA1_RABIT 11: ---------------------------------MARKPLLHYFNGRGRMESIRWLLAAAG 11: EEFDEKFMETAEDLDKLRNDG--SLMYQQVPMVEI-----DG--MKLVQTRAILNYVA-- 11: NKHNLY-GKDMKER--------ALIDMYTE-GVADLYELVLLLPLCP------------- 11: -PEQKDAKVDFIKEK-IRTRYFPAFEKVLKSH--GQDYL-VGNRLSKADILLVELLYN-- 11: -----VEE--LDPSAIA--S-FPLLKALKTRI-SSLPTVKKFLQPGSQRKPPMDEKNLEK 11: AKKIFKIP------ 11: >GTA1_CAVPO 11: ----------------------------------SGKPVLHYFNVQGRMESIRWLLAAAG 11: VEFEEKLIMCQEDLDKLKNDG--LLMFQQVPMVEM-----DG--MKMVQSRAILNYIA-- 11: TKYNLY-GKDTKER--------LLIDMYTE-GMTDLYELFFKVILAP------------- 11: -PEEKDAAKSLIKDR-AKNRFLPAFEKVLKSH--GQGYL-VGNKLSKADILLTELLYM-- 11: -----VEE--FDASLLA--N-FTLLQALKTRV-SNLPNVKKFLQPGSQRKPFPTQEMFEE 11: MRKF---------- 11: >GTA3_RAT 11: ---------------------------------MEVKPKLYYFQGRGRMESIRWLLATAG 11: VEFEEEFLETREQYEKLQKDG--CLLFGQVPLVEI-----DG--MLLTQTRAILSYLA-- 11: AKYNLY-GKDLKER--------VRIDMYAD-GTQDLMMMIIGAPFKA------------- 11: -PQEKEESLALAVKR-AKNRYFPVFEKILKDH--GEAFL-VGNQLSWADIQLLEAILM-- 11: -----VEE--VSAPVLS--D-FPLLQAFKTRI-SNIPTIKKFLQPGSQRKPPPDGHYVDV 11: VRTVLKF------- 11: >GTA3_CHICK 11: ----------------------------------AAKPVLYYFNGRGKMESIRWLLAAAG 11: VEFEEVFLETREQYEKLLQSG--ILMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- 11: GKYNLY-GKDLKER--------ALIDMYVG-GTDDLMGFLLSFPFLS------------- 11: -AEDKVKQCAFVVEK-ATSRYFPAYEKVLKDH--GQDFL-VGNRLSWADIHLLEAILM-- 11: -----VEE--KKSDALS--G-FPLLQAFKKRI-SSIPTIKKFLAPGSKRKPISDDKYVET 11: VRRVLRMYYDVKPH 11: >GTA2_CHICK 11: ---------------------------------MAGKPKLHYTRGRGKMESIRWLLAAAG 11: VEFEEEFIEKKEDLEKLRNDG--SLLFQQVPMVEI-----DG--MKMVQSRAILCYIA-- 11: GKYNLY-GKDLKER--------AWIDMYVE-GTTDLMGMIMALPFQA------------- 11: -ADVKEKNIALITER-ATTRYFPVYEKALKDH--GQDYL-VGNKLSWADIHLLEAILM-- 11: -----TEE--LKSDILS--A-FPLLQAFKGRM-SNVPTIKKFLQPGSQRKPPLDEKSIAN 11: VRKIFSF------- 11: >GTA1_CHICK 11: ---------------------------------MSGKPVLHYANTRGRMESVRWLLAAAG 11: VEFEEKFLEKKEDLQKLKSDG--SLLFQQVPMVEI-----DG--MKMVQTRAILNYIA-- 11: GKYNLY-GKDLKER--------ALIDMYVE-GLADLYELIMMNVVQP------------- 11: -ADKKEEHLANALDK-AANRYFPVFEKVLKDH--GHDFL-VGNKLSRADVHLLETILA-- 11: -----VEE--SKPDALA--K-FPLLQSFKART-SNIPNIKKFLQPGSQRKPRLEEKDIPR 11: LMAIFH-------- 11: >GTA1_ANTST 11: ---------------------------------MAGEQNIKYFNIKGRMEAIRWLLAVAG 11: VEFEEKFFETKEQLQKLKET---VLLFQQVPMVEI-----DG--MKLVQTRAILHYIA-- 11: EKYNLL-GKDMKEH--------AQIIMYSE-GTMDLMELIMIYPFLK------------- 11: -GEEKKQRLVEIANK-AKGRYFPAFENVLKTH--GQNFL-VGNQLSMADVQLFEAILM-- 11: -----VEE--KVPDALS--G-FPLLQAFKTRI-SNIPTVKTFLAPGSKRKPVPDAKYVED 11: IIKIFYF------- 11: >GTA4_HUMAN 11: ---------------------------------MAARPKLHYPNGRGRMESVRWVLAAAG 11: VEFDEEFLETKEQLYKLQDGN--HLLFQQVPMVEI-----DG--MKLVQTRSILHYIA-- 11: DKHNLF-GKNLKER--------TLIDMYVE-GTLDLLELLIMHPFLK------------- 11: -PDDQQKEVVNMAQK-AIIRYFPVFEKILRGH--GQSFL-VGNQLSLADVILLQTILA-- 11: -----LEE--KIPNILS--A-FPFLQEYTVKL-SNIPTIKRFLEPGSKKKPPPDEIYVRT 11: VYNIFRP------- 11: >1oe7_A 11: -----------------------------------DHIKVIYFNGRGRAESIRMTLVAAG 11: VNYEDERISF-QDWPKIKP----TIPGGRLPAVKITDNHGHV--KWMVESLAIARYMA-- 11: KKHHMM-GGTEEEY--------YNVEKLIG-QAEDLEHEYYKTLMKP------------- 11: -EEEKQKIIKEILNG-KVPVLLDIICESLKAS--TGKLA-VGDKVTLADLVLIAVIDH-- 11: -----VTD--LDKEFLT--GKYPEIHKHRENLLASSPRLAKYL---SDRA---------- 11: -------------- 11: >GTP1_BUFBU 11: -----------------------------------PEYTIIYFNARGRCEAMRMLMADQG 11: AQWKEEVVTS-DDWQKGDLKK--AAVYGQLPGFK------DGD-FTLYQSNAMLRLLA-- 11: RNHDLY-GKNPREA--------SLIDMVND-GVEDLRLKYLKMIYQN------------- 11: -YENGKDDYV----K-ALPTNLGHFERLLASNNEGKGFV-VGAHISFADYNLVDLLHN-- 11: -----HLV--LAPDCLS--G-FPLLCAYVKRI-SSRPKLEAYLSSDAHKKRPINGNGKQQ 11: -------------- 11: >GT28_SCHJA 11: -------------------------------------VKLIYFNGRGRAEPIRMILVAAG 11: VEFEDERIEF-QDWPKIKP----TIPGGRLPIVKITDKRGDV--KTMSESLAIARFIA-- 11: RKHNMM-GDTDDEY--------YIIEKMIG-QVEDVESEYHKTLIKP------------- 11: -PEEKEKISKEILNG-KVPILLQAICETLKES--TGNLT-VGDKVTLADVVLIASIDH-- 11: -----ITD--LDKEFLT--GKYPEIHKHRKHLLATSPKLAKYL---SERHATAF------ 11: -------------- 11: >GTS1_ASCSU 11: -----------------------------------PQYKLTYFDIRGLGEGARLIFHQAG 11: VKFEDNRLKR-EDWPALKP----KTPFGQLPLLEV-----DGE--VLAQSAAIYRYLG-- 11: RQFGLA-GKTPMEE--------AQVDSIFD-QFKDFMAELRPC-FRV-----LAGFE--- 11: -EGDKEKVLKEVAVP-ARDKHLPLLEKFLA--KSGSEYM-VGKSVTWADLVITDSLAS-- 11: -----WES--LIPDFLS--G-HLQLKKYIEHV-RELPNIKKWIAERPKTPY--------- 11: -------------- 11: >GTS9_CAEEL 11: ----------------------------------MVSYKLIYFQSRGNGEIARQVFAFAG 11: QEFIDERISK-EQWAEIKN----MTPFGQVPVLEV-----DGR--QLAQSITIVRYLS-- 11: KQFGIS-GKSSWEE--------AQVDALGD-QFKDYRVEARPF-FRA-----KMGFS--- 11: -DGDVDQLYKDLFVP-AFNKMYSIFTESLK--SSGSGFL-VGDSLTWMDLAIAQHSAD-- 11: -----LLE--ADGKILD--T-FLEMKDHQKKI-HSIPNVKKWIEKRPVTSR--------- 11: -------------- 11: >GTS3_CAEEL 11: ----------------------------------MVHYKLTYFNARGLAEISRQLFHMAG 11: VEFEDERINE-EKFSQLKP----TFPSGQVPILCI-----DGA--QFSQSTAIARYLA-- 11: RKFGFV-GQTAEEE--------LQADEVVD-TFKDFIESFRKFVIAV-----LSGES--- 11: -EEILKNIREEVIKP-AVKTYTAYLKAILE--KSSSGYL-VGNELTWADLVIADNLTT-- 11: -----LIN--AELLDIE--N-DKLLKEFREKI-IETPKLKEWLAKRPETRF--------- 11: -------------- 11: >GTS5_CAEEL 11: ----------------------------------MVSYKLTYFNGRGAGEVSRQIFAYAG 11: QQYEDNRVTQ-EQWPALKETC--AAPFGQLPFLEV-----DGK--KLAQSHAIARFLA-- 11: REFKLN-GKTAWEE--------AQVNSLAD-QYKDYSSEARPY-FYA-----VMGFG--- 11: -PGDVETLKKDIFLP-AFEKFYGFLVNFLK--ASGSGFL-VGDSLTWIDLAIAQHSAD-- 11: -----LI---AKGGDFS--K-FPELKAHAEKI-QAIPQIKKWIETRPVTPF--------- 11: -------------- 11: >GTS6_CAEEL 11: ----------------------------------MVHYKLVYFPLRARAEIARQIFAYAG 11: QDYSEENLSF-EQWPARKN----NTPFGQLPILEV-----DGK--PLGQSYAIARYLA-- 11: REFGIA-GQNDTEA--------AEVDAIAD-QFKDYLNDVSPY-LTV-----LAGFK--- 11: -PGDKDQLRTDVFVP-AFKKNFEFFENILA--SNHSGFF-VGNSLTWVDLLISQHVQD-- 11: -----ILD--KDLAVVE--E-FKKVLAHRKKV-QSIDRIQKYIANRPDYPF--------- 11: -------------- 11: >GTS4_CAEEL 11: ----------------------------------MPNYKLLYFDARALAEPIRIMFAMLN 11: VPYEDYRVSV-EEWSKLKP----TTPFGQLPILQV-----DGE--QFGQSMSITRYLA-- 11: RKFGLA-GKTAEEE--------AYADSIVD-QYRDFIFFFRQFTSSV-----FYGSD--- 11: -ADHINKVRFEVVEP-ARDDFLAIINKFLA--KSKSGFL-VGDSLTWADIVIADNLTS-- 11: -----LLK--NGFLDFN--K-EKKLEEFYNKI-HSIPEIKNYVATRKDSIV--------- 11: -------------- 11: >GTS2_CAEEL 11: ----------------------------------MVHYKLMCFDVRGLGEVIRQLFYLGD 11: VSFEDFRVSR-EEFKSLKS----NLPSGQLPVLEI-----DGV--MISQSASIGRFLA-- 11: RQYGYS-GKTPTEE--------MQVDSIID-LFKDFMLTFRQFFFAV-----IHGYP--- 11: -EYEKERMKRDIVKP-AIKNYFIALNKILL--RSKSGFL-VGDDLTWADLQIADNLST-- 11: -----LIN--IRLF-AE--K-EPHLNVFIRKL---------------------------- 11: -------------- 11: >GTS1_CAEEL 11: ----------------------------------MPHFKFYYFDVRGRGEAIRLLFHLAD 11: EKFDDERFGM-EQWGVLKS----EMPLGQVPVLEI-----DGV--KISQTTAIARYLG-- 11: HQFHRA-GTNAVDC--------ARLDMIAE-VIQEFMSSSGMGKFSR----VLLGMI--- 11: -QANKEQFFKENVLP-DVEKYAPIVEKFLL-ENGNNGLL-LGDRETWVDVFAAESFSK-- 11: -----LIDY-GSPDALD--A-YPHILALINRV-FNHPNIKKYVSQRKATPA--------- 11: -------------- 11: >GTS_ANOGA 11: -------------------LSSSSISRSSLKCNIMPDYKVYYFNVKALGEPLRFLLSYGN 11: LPFDDVRITR-EEWPALKP----TMPMRQMPVLEV-----DGK--RVHQSLAMCRYVA-- 11: KQINLA-GDNPLEA--------LQIDAIVD-TINDFRLKIAIVAYEP------DDMV--- 11: -KEKKMVTLNNEVIPFYLTKLNVIAKE-------NNGHL-VLGKPTWADVYFAGILDY-- 11: -----L-NYLTKTNLLE--N-FPNLQEVVQKV-LDNENVKAYIAKRPITEV--------- 11: -------------- 11: >GTS2_MANSE 11: ----------------------------------MPKVVFHYFGAKGWARP-TMLLAYGG 11: QEFEDHRVEY-EQWPEFKP----NTPFGQMPVLEI-----DGK--KYAQSLAISRYLG-- 11: RKYGLA-GNDIEED--------FEIDQIVD-FVNDIRASAASVEYEQ------DAAN--- 11: -KEVKHEENMKNKYPFQLNKLSEIITK-------NNGFL-ALGRLTWADFVFVGMFDY-- 11: -----LKKMLRMPDLEE--Q-YPIFKKPIETV-LSNPKLKAYLDSAPKKEF--------- 11: -------------- 11: >GT1_ONCVO 11: FITMNFVVEAASSNANQAITSENSIKPKGKLQPQMEKYTLTYFNGRGRAEVIRLLFALAN 11: VSYEDNRITR-DEWKYLKP----RTPFGHVPMLNV-----SGN--VLGESHAIELLLG-- 11: GRFGLL-GTNDWEE--------AKIMAVVL-NIDELFQKLIPWTHEK-----NTTKK--- 11: -AELFRNLSESDVMP-FLGRY----EKFLK--ESTTGHI-VGNKVSVADLTVFNMLMT-- 11: -----L----DDEVKLE--E-YPQLASFVNKI-GQMPGIKEWIKKRPKTYF--------- 11: -------------- 11: >SC11_OMMSL 11: ----------------------------------MPSYTLYYFNGRGRAEICRMLFAVAS 11: VQYQDKRIEL-AEWTQFKT----KMPCHMLPILEI-----DTE-TQVPQSMAISRYLA-- 11: REFGFY-GKNNMDM--------FKVDCLCD-SLFELFNDYMAVYNEK------------- 11: -DAAKKTELQKRFQN-TCLRVLPYMEKTLEANKGGAGWF-IGDQILLCDMMTHAALEN-- 11: -----PIQ--ENANLLK--E-YPKLAALRTRV-AAHPKIAAYIKKRNNTAF--------- 11: -------------- 11: >SC2_OCTDO 11: ----------------------------------MPSYTLNYFNHRGRAEICRMLFAAAG 11: VQYNDRRIET-SEWSNMRS----KMPCSMMPMLDI-----DNR-HQIPQTMAIARYLA-- 11: REFGFH-GKNNMEM--------ARVEYISD-CFYDILDDYLRMYQDDNCRMMFQRSG--- 11: -DRNGSSEKRTRYQE-TLRRILPFMERTLEMYKSGGQFF-MGDQMTMADMMCYCALEN-- 11: -----PIM--EESSLLN--S-YPKLQALRTRV-MSHLKMSPYLKKRSSTEF--------- 11: -------------- 11: >1aw9_ 11: ----------------------------------AP-LKLYGMPLSPNVVRVATVLNEKG 11: LDFEIVPVDLTTGAHKQPDFL-ALNPFGQIPALV------DGD-EVLFESRAINRYIA-- 11: SKYASE-GTDLLPATASA----AKLEVWLEVESHHFYPNASPLVFQL----LVRPLL--- 11: -GGAPDAAVVDKHAE-QLAKVLDVYEAHLA----RNKYL-AGDEFTLADANHASYLLY-- 11: -----L-SKTPKAGLVA--A-RPHVKAWWEAI-VARPAFQKTVAAIPLPPPP-------- 11: -------------- 11: >GTH3_ARATH 11: -----------------------------------V-LTIYA-PLFASSKRAVVTLVEKG 11: VSFETVNVDLMKGEQRQPEYL-AIQPFGKIPVLV------DGD-YKIFESRAIMRYIA-- 11: EKYRSQ-GPDLLGKTIEER---GQVEQWLDVEATSYHPPLLALTLNI----VFAPLM--- 11: -GFPADEKVIKESEE-KLAEVLDVYEAQLS----KNEYL-AGDFVSLADLAHLPFTEY-- 11: -----LVGPIGKAHLIK--D-RKHVSAWWDKI-SSRAAWKEVSAKYSLPV---------- 11: -------------- 11: >GTH7_ARATH 11: ----------------------------------MV-VKVYGQIKAANPQRVLLCFLEKD 11: IEFEVIHVDLDKLEQKKPQHL-LRQPFGQVPAIE------DGY-LKLFESRAIARYYA-- 11: TKYADQ-GTDLLGKTLEGR---AIVDQWVEVENNYFYAVALPLVMNV----VFKPKS--- 11: -GKPCDVALVEELKV-KFDKVLDVYENRLA----TNRYL-GGDEFTLADLSHMPGMRY-- 11: -----IMNETSLSGLVT--S-RENLNRWWNEI-SARPAWKKLMELAAY------------ 11: -------------- 11: >GTH6_ARATH 11: ---------------------------------MAS-IKVHGVPMSTATMRVLATLYEKD 11: LQFELIPVDMRAGAHKQEAHL-ALNPFGQIPALE------DGD-LTLFESRAITQYLA-- 11: EEYSEK-GEKLISQDCKKVK--ATTNVWLQVEGQQFDPNASKLAFER----VFKGMF--- 11: -GMTTDPAAVQELEG-KLQKVLDVYEARLA----KSEFL-AGDSFTLADLHHLPAIHY-- 11: -----LLGTDSKV-LFD--S-RPKVSEWIKKI-SARPAWAKVIDLQKQ------------ 11: -------------- 11: >GTH_SILCU 11: -----------------------------------T-IKVHGNPRSTATQRVLVALYEKH 11: LEFEFVPIDMGAGGHKQPSYL-ALNPFGQVPALE------DGE-IKLFESRAITKYLAYT 11: HDHQNE-GTSLIHKE-KHEM--AAQLVWEEVEAHQFDPVASKLAWEL----VFKGIF--- 11: -GMQTDTTVVEENEA-KLAKVLDVYEARLT----ESEYLGANDSFTLVDLHHLPLLGY-- 11: -----LMGTQVKK-LFE--E-RAHVSAWCKKI-LARPSWEKTLALQKQA----------- 11: -------------- 11: >GTH1_ARATH 11: ---------------------------------MAG-IKVFGHPASTATRRVLIALHEKN 11: VDFEFVHVELKDGEHKKEPFI-LRNPFGKVPAFE------DGD-FKIFESRAITQYIA-- 11: HEFSDK-GNNLLST-GKDM---AIIAMGIEIESHEFDPVGSKLVWEQ----VLKPLY--- 11: -GMTTDKTVVEEEEA-KLAKVLDVYEHRLG----ESKYL-ASDHFTLVDLHTIPVIQY-- 11: -----LLGTPTKK-LFD--E-RPHVSAWVADI-TSRPSAQKVL----------------- 11: -------------- 11: >GTH4_ARATH 11: ----------------------------------AG-IKVFGHPASIATRRVLIALHEKN 11: LDFELVHVELKDGEHKKEPFL-SRNPFGQVPAFE------DGD-LKLFESRAITQYIA-- 11: HRYENQ-GTNLLQTDSKNISQYAIMAIGMQVEDHQFDPVASKLAFEQ----IFKSIY--- 11: -GLTTDEAVVAEEEA-KLAKVLDVYEARLK----EFKYL-AGETFTLTDLHHIPAIQY-- 11: -----LLGTPTKK-LFT--E-RPRVNEWVAEI-TKRPASEKVQ----------------- 11: -------------- 11: >GTH4_MAIZE 11: ---------------------------------ATPAVKVYGWAISPFVSRALLALEEAG 11: VDYELVPMSRQDGDHRRPEHL-ARNPFGKVPVLE------DGD-LTLFESRAIARHVL-- 11: RKHKP----ELLGGGR-LEQT-AMVDVWLEVEAHQLSPPAIAIVVEC----VFAPFL--- 11: -GRERNQAVVDENVE-KLKKVLEVYEARLA----TCTYL-AGDFLSLADLSPFTIMHC-- 11: -----LMATEYAA-LVH--A-LPHVSAWWQGL-AARPAANKVAQFMPVGAGAPKEQE--- 11: -------------- 11: >GTH1_MAIZE 11: ---------------------------------A-P-MKLYGAVMSWNLTRCATALEEAG 11: SDYEIVPINFATAEHKSPEHL-VRNPFGQVPALQ------DGD-LYLFESRAICKYAA-- 11: RKNKP----ELLREGN-LEEA-AMVDVWIEVEANQYTAALNPILFQV----LISPML--- 11: -GGTTDQKVVDENLE-KLKKVLEVYEARLT----KCKYL-AGDFLSLADLNHVSVTLC-- 11: -----LFATPYAS-VLD--A-YPHVKAWWSGL-MERPSVQKVAALMKPSA---------- 11: -------------- 11: >GTH1_WHEAT 11: ---------------------------------MSP-VKVFGHPMLTNVARVLLFLEEVG 11: AEYELVPMDFVAGEHKRPQHV-QLNPFAKMPGFQ------DGD-LVLFESRAIAKYIL-- 11: RKYGGTAGLDLLGENSGIEEL-AMVDVWTEVEAQQYYPAISPVVFEC----IIIPFIIPG 11: GGAAPNQTVVDESLE-RLRGVLGIYEARLE----KSRYL-AGDSITFADLNHIPFTFY-- 11: -----FMTTPYAK-VFD--D-YPKVKAWWEML-MARPAVQRVCKHMPTEFKLGAQY---- 11: -------------- 11: >GTH5_ARATH 11: ---------------------------------MVT-VKLYGMAYSTCTKRVYTTAKEIG 11: VDVKIVPVDLMKGEHKEPAYLDNYHPFGVIPVLE------DEDGTKIYESRAISRYLV-- 11: AKYGK--GSSLLPSPSDPKAY-GLFEQAASVEYSSFDPPASSLAYER----VFAGMR--- 11: -GLKTNEELAKKYVD-TLNAKMDGYERILS----KQKYL-AGNDFTLADLFHLPY-GA-- 11: -----MVAQLEPT-VLD--S-KPHVKAWWAA--SLRVIPGRLLRNSSKEFM--------- 11: -------------- 11: >1eem_A 11: ---------------SARSLGKGSAPPGPV---PEGSIRIYSMRFCPFAERTRLVLKAKG 11: IRHEVININLKNKPEWFFK----KNPFGLVPVLENS----QGQ--LIYESAITCEYLD-- 11: EAYP---GKKLLPDDPYEK---ACQKMILE-LFSKVPSLVGSFIRSQ------------- 11: -N-KEDYAGLKE----EFRKEFTKLEEVLTNK--KTTFF-GGNSISMIDYLIWPWFER-- 11: -----LEAM-KLNECVD--H-TPKLKLWMAAM-KEDPTVSALLTSEKDWQGFLE-LYLQN 11: SPEACDYGL----- 11: >GTO1_MOUSE 11: -----------MSGESSRSLGKGSAPPGPV---PEGQIRVYSMRFCPFAQRTLMVLKAKG 11: IRHEVININLKNKPEWFFE----KNPLGLVPVLENS----QGH--LVTESVITCEYLD-- 11: EAYP---EKKLFPDDPYKK---ARQKMTLE-SFSKVPPLIASFVRSK------------- 11: -R-KEDSPNLRE----ALENEFKKLEEGMDNY--K-SFL-GGDSPSMVDYLTWPWFQR-- 11: -----LEAL-ELKECLA--H-TPKLKLWMAAM-QQDPVASSHKIDAKTYREYLN-LYLQD 11: SPEACDYGL----- 11: >GTO2_HUMAN 11: -----------MSGDATRTLGKGSQPPGPV---PEGLIRIYSMRFCPYSHRTRLVLKAKD 11: IRHEVVNINLRNKPEWYYT----KHPFGHIPVLETS----QCQ--LIYESVIACEYLD-- 11: DAYP---GRKLFPYDPYER---ARQKMLLE-LFCKVPHLTKECLVAL------------- 11: -RCGRECTNLKA----ALRQEFSNLEEILEYQ--NTTFF-GGTCISMIDYLLWPWFER-- 11: -----LDVY-GILDCVS--H-TPALRLWISAM-KWDPTVCALLMDKSIFQGFLN-LYFQN 11: NPNAFDFGLC---- 11: >YKJ3_CAEEL 11: -------------------MTVLAGVNSKIVKNGCWNHSYLQHAILPVAQRALIYASVKN 11: IPSDVINVHLQEKPDWYFS----KHYKGQVPTLEHD----EGK-KHVIESAVIPEYLD-- 11: DIYP---ETRILPTDPYEK---VQQKLLLDRISGQVSPAFYGVVQAV------------- 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI 10/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.15 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2023-04-28 00:26:32] : LOG : Testing correctness of AVX bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: Dyn AVX DYN/AVX 1: [2023-04-28 00:26:42] : LOG : Timing DYN 256 1: [2023-04-28 00:26:46] : LOG : 3.270155 - dyn 1: [2023-04-28 00:26:46] : LOG : 0.000000 - bpm 1: [2023-04-28 00:26:46] : LOG : 0.210979 - bpm_block2 1: [2023-04-28 00:26:46] : LOG : 0.220022 - bpm_block 11/11 Test #1: bpm_utest ........................ Passed 13.57 sec 100% tests passed, 0 tests failed out of 11 Total Test time (real) = 13.57 sec make[2]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/kalign-3.3.5' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/kalign-3.3.5/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/kalign-3.3.5/debian/kalign/usr/lib/aarch64-linux-gnu/libkalign.a -- Installing: /build/kalign-3.3.5/debian/kalign/usr/include/kalign/kalign.h -- Installing: /build/kalign-3.3.5/debian/kalign/usr/include/kalign/kalign_export.h -- Installing: /build/kalign-3.3.5/debian/kalign/usr/lib/aarch64-linux-gnu/cmake/kalign/kalignTargets.cmake -- Installing: /build/kalign-3.3.5/debian/kalign/usr/lib/aarch64-linux-gnu/cmake/kalign/kalignTargets-none.cmake -- Installing: /build/kalign-3.3.5/debian/kalign/usr/lib/aarch64-linux-gnu/cmake/kalign/kalignConfig.cmake -- Installing: /build/kalign-3.3.5/debian/kalign/usr/lib/aarch64-linux-gnu/cmake/kalign/kalignConfigVersion.cmake -- Installing: /build/kalign-3.3.5/debian/kalign/usr/bin/kalign make[1]: Leaving directory '/build/kalign-3.3.5/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/kalign-3.3.5' dh_install rm -rf debian/kalign/usr/lib/aarch64-linux-gnu/ dh_install obj-aarch64-linux-gnu/src/kalignfmt usr/bin make[1]: Leaving directory '/build/kalign-3.3.5' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Built-Using field of package kalign: substitution variable ${simde:Built-Using} used, but is not defined dpkg-gencontrol: warning: Built-Using field of package kalign: substitution variable ${simde:Built-Using} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'kalign' in '../kalign_3.3.5-1_arm64.deb'. dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3.5-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.3.5-1_arm64.buildinfo dpkg-genchanges --build=binary -O../kalign_3.3.5-1_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/10190 and its subdirectories I: Current time: Fri Apr 28 00:26:56 -12 2023 I: pbuilder-time-stamp: 1682684816 Fri Apr 28 12:26:58 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink9-arm64.debian.net. Fri Apr 28 12:26:58 UTC 2023 I: Preparing to do remote build '2' on codethink9-arm64.debian.net. Fri Apr 28 12:28:11 UTC 2023 I: Deleting $TMPDIR on codethink9-arm64.debian.net. Fri Apr 28 12:28:11 UTC 2023 I: kalign_3.3.5-1_arm64.changes: Format: 1.8 Date: Mon, 06 Feb 2023 07:35:19 +0100 Source: kalign Binary: kalign kalign-dbgsym Architecture: arm64 Version: 1:3.3.5-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: kalign - Global and progressive multiple sequence alignment Changes: kalign (1:3.3.5-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 93c43ce4cd85af7cf7afb5fd8796e61c0da70d49 207624 kalign-dbgsym_3.3.5-1_arm64.deb 01d90ca28892b72406298039d83b507b06a6f975 5848 kalign_3.3.5-1_arm64.buildinfo c938141dae88ef23a9e86d6856233bc5727f64fa 82980 kalign_3.3.5-1_arm64.deb Checksums-Sha256: 33a9fdd65810a11528f0fb765706af7fc72d7995740bd85935b1a1c13728bd56 207624 kalign-dbgsym_3.3.5-1_arm64.deb 5ec1ce0d098c91037157b827fc21618830dee615d1cc0bead29751b234a9681c 5848 kalign_3.3.5-1_arm64.buildinfo 14b38aeb135bf898ac3f74926ee1d0a4568af533881f6bfc9be6cc7efb044641 82980 kalign_3.3.5-1_arm64.deb Files: a9026683c14cc2f5fb661bf43695305a 207624 debug optional kalign-dbgsym_3.3.5-1_arm64.deb 655c0fbb67ee11ffbe3e023183bb116a 5848 science optional kalign_3.3.5-1_arm64.buildinfo bcf6b96395fa97bb643c17fb8d117904 82980 science optional kalign_3.3.5-1_arm64.deb Fri Apr 28 12:28:16 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.NIWpP6so/kalign_3.3.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.NIWpP6so/kalign_3.3.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.NIWpP6so/kalign_3.3.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.NIWpP6so/b1/kalign_3.3.5-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.NIWpP6so/b2/kalign_3.3.5-1_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: 0.355s) 0.355s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.020s) 0.020s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Apr 28 12:28:22 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 28 12:28:22 UTC 2023 I: kalign from bookworm built successfully and reproducibly on arm64. Fri Apr 28 12:28:24 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 28 12:28:24 UTC 2023 I: Submitting 8.0K b1/kalign_3.3.5-1_arm64.buildinfo.asc Fri Apr 28 12:28:26 UTC 2023 I: Submitting 8.0K b2/kalign_3.3.5-1_arm64.buildinfo.asc Fri Apr 28 12:28:27 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 28 12:28:27 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 28 12:28:27 UTC 2023 I: Removing signed kalign_3.3.5-1_arm64.buildinfo.asc files: removed './b1/kalign_3.3.5-1_arm64.buildinfo.asc' removed './b2/kalign_3.3.5-1_arm64.buildinfo.asc'