Running as unit: rb-build-amd64_6-52134.service ==================================================================================== Thu Jul 31 04:32:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_6) on jenkins, called using "ionos5-amd64 ionos11-amd64" as arguments. Thu Jul 31 04:32:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-iCi7rdze" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 04:32:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Jul 31 04:32:33 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-r26Mnn' Thu Jul 31 04:32:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Jul 31 04:32:33 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-14A5cl' ok, let's check if kalign is building anywhere yet… ok, kalign is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of kalign in trixie on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Thu Jul 31 04:32:50 UTC 2025 I: starting to build kalign/trixie/amd64 on jenkins on '2025-07-31 04:32' Thu Jul 31 04:32:50 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_6/52134/console.log 1753936370 amd64 trixie kalign Thu Jul 31 04:32:50 UTC 2025 I: Downloading source for trixie/kalign=1:3.4.0-1 --2025-07-31 04:32:50-- http://deb.debian.org/debian/pool/main/k/kalign/kalign_3.4.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1962 (1.9K) [text/prs.lines.tag] Saving to: ‘kalign_3.4.0-1.dsc’ 0K . 100% 241M=0s 2025-07-31 04:32:50 (241 MB/s) - ‘kalign_3.4.0-1.dsc’ saved [1962/1962] --2025-07-31 04:32:50-- http://deb.debian.org/debian/pool/main/k/kalign/kalign_3.4.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1962 (1.9K) [text/prs.lines.tag] Saving to: ‘kalign_3.4.0-1.dsc’ 0K . 100% 241M=0s 2025-07-31 04:32:50 (241 MB/s) - ‘kalign_3.4.0-1.dsc’ saved [1962/1962] Thu Jul 31 04:32:50 UTC 2025 I: kalign_3.4.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kalign Binary: kalign Architecture: any Version: 1:3.4.0-1 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: 3a843c18bd6337b80b373815e2ec4b73ce53f3ab 903277 kalign_3.4.0.orig.tar.gz 580fd65a94ca1e2cc4bcd70588708fa680c5195f 12372 kalign_3.4.0-1.debian.tar.xz Checksums-Sha256: 67d1a562d54b3b7622cc3164588c05b9e2bf8f1a5140bb48a4e816c61a87d4a8 903277 kalign_3.4.0.orig.tar.gz 83643a83685ef7b3da11348ccb6d3b5c22478547b46a8b88288530a6c00cf8bc 12372 kalign_3.4.0-1.debian.tar.xz Files: 52243b10203d6ce97ade643638571c1e 903277 kalign_3.4.0.orig.tar.gz 6a79c99575fec3b663aa9b0ce68b277e 12372 kalign_3.4.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYL8UcACgkQPCZ2P2xn 5uIriw//TWTZYvOK72oNuNPUktDVviVZq8AV8m0P0gCb/LHX04PB76lT2j3qBStq KBkSwq4Wb9CvGXBvHUooQldK/yT7Y1elltnTDOhMXGwHsgBemF8zBUY1Cc3miXEu 4dF5pKd327uo4HROZqPkEWHMEcxq7ldXYdvbjFKqsKNqNvjLvEcrFOKtIIdaKpCm ImRJnFYEXiQwskUHjZjnnM0V59o4ZjizgQfxt1T/YpGzKx4xV9S6LbHQ2jf0VVf4 dZ2KEvjN9IhMEcOfPIVWj4V22IXQKp3QQV0JyVWz0jommBpVAENpigftCSvQTv7s +Ff4XcJQshiF+h8gZDTuneTCruS2wBYNS9gU127hKZ/dD8T34N0o80xnxll2ETLE KaMH5CIWMNUqd3vwNUm6RJXfvswY5KAf+iPShTkXNAsZbXHcNRVoZNtIY5FoSNt1 dvu5SfIXJjWpzhBPjBh+V2N974UYw+GSUAraWVNKAjnUJGiyyo9bLgDwNT0imPgh k/is6QD0s7KFQMT86HshRfEXpVsvbzvZ4a33jSMROInA6bwZDh2ugnYYKLvyDJM3 ZhdV4pptTaHbo6clU+2c2sLJekNLP6lwCBfA/0AzOyVzacAuJ16oPk85LmcExZVH ROh0Ts3BkKOTpRCs0vrlN0Ikcb1pEGxjjyvnUsO+VWjwFSWBq68= =OLrO -----END PGP SIGNATURE----- Thu Jul 31 04:32:50 UTC 2025 I: Checking whether the package is not for us Thu Jul 31 04:32:50 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Jul 31 04:32:50 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Jul 31 04:32:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Jul 31 04:32:50 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Z6mngn' ==================================================================================== Wed Sep 2 10:55:51 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 kalign trixie /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ 1:3.4.0-1" as arguments. Wed Sep 2 10:55:51 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-q1zpyvmK" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 2 10:55:51 UTC 2026 I: Downloading source for trixie/kalign=1:3.4.0-1 Reading package lists... NOTICE: 'kalign' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kalign.git Please use: git clone https://salsa.debian.org/med-team/kalign.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 918 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (dsc) [1962 B] Get:2 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (tar) [903 kB] Get:3 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (diff) [12.4 kB] Fetched 918 kB in 0s (31.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'kalign' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kalign.git Please use: git clone https://salsa.debian.org/med-team/kalign.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 918 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (dsc) [1962 B] Get:2 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (tar) [903 kB] Get:3 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (diff) [12.4 kB] Fetched 918 kB in 0s (31.5 MB/s) Download complete and in download only mode ============================================================================= Building kalign in trixie on amd64 on ionos5-amd64 now. Date: Wed Sep 2 10:55:51 UTC 2026 Date UTC: Wed Sep 2 10:55:51 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 1 22:55:51 -12 2026 I: pbuilder-time-stamp: 1788346551 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kalign_3.4.0-1.dsc] I: copying [./kalign_3.4.0.orig.tar.gz] I: copying [./kalign_3.4.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./kalign_3.4.0-1.dsc: no acceptable signature found dpkg-source: info: extracting kalign in kalign-3.4.0 dpkg-source: info: unpacking kalign_3.4.0.orig.tar.gz dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8fee02fc933e4602b39349a6300fdb23' 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='1867936' 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.u98MuRLQ/pbuilderrc_uT3F --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-8 [881 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b2 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 31.9 MB in 6s (5250 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-8_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-8_amd64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/kalign-3.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kalign_3.4.0-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.4.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/reproducible-path/kalign-3.4.0' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (4.7s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-sse4.1 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-sse4.1 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (9.3s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-sse4.1 dh_auto_configure --builddirectory obj-avx -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF cd obj-avx && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (11.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx dh_auto_configure --builddirectory obj-avx2 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON cd obj-avx2 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- Performing Test HAVE_AVX2 -- Performing Test HAVE_AVX2 - Success -- AVX2 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (7.9s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx2 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 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/build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 10%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 14%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 14%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 16%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 17%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 21%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c [ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 24%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 27%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 33%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 41%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 66%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 [ 67%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 68%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection 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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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign_static.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 74%] Built target kalign [ 74%] Built target kalign_static make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/kalign_io_test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests 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/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -MF CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o.d -o CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_io_test.c make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -MF CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o.d -o CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/c++ -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -MF CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o.d -o CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -MF CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o.d -o CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_cmp_test.c make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests 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src/CMakeFiles/kalignfmt.dir/parameters.c.o [ 87%] Building C object src/CMakeFiles/kalign-bin.dir/parameters.c.o [ 89%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/largebench.dir/large_benchmark.c.o -MF CMakeFiles/largebench.dir/large_benchmark.c.o.d -o CMakeFiles/largebench.dir/large_benchmark.c.o -c /build/reproducible-path/kalign-3.4.0/tests/large_benchmark.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim_test.c.o -MF CMakeFiles/dssim.dir/dssim_test.c.o.d -o CMakeFiles/dssim.dir/dssim_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd 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'/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 93%] Built target kalign_cmp_test [ 93%] Built target kalign_io_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f 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lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 13%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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-DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 20%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 21%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o 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/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 27%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c [ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 64%] 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/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 67%] Linking C static library libkalign_static.a [ 67%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 [ 70%] Linking C executable task_utest [ 71%] Linking C executable alphabet_utest [ 72%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 74%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kalign_cmp_test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kaligncpp.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/build make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 79%] Building C object tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o [ 79%] Building CXX object tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o [ 79%] Built target tldevel cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -MF CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o.d -o CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_io_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/c++ -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -MF 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Building C object tests/CMakeFiles/dssim.dir/dssim.c.o [ 83%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim_test.c.o -MF CMakeFiles/dssim.dir/dssim_test.c.o.d -o CMakeFiles/dssim.dir/dssim_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. 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94%] Linking C executable kalign cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 [ 98%] Linking C executable largebench [ 98%] Linking C executable kalignfmt [ 98%] Linking C executable dssim cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 98%] Built target kalign-bin /usr/bin/cc -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 1%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 5%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 6%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 18%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 20%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 22%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd 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/build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 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lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 12%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 56%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 56%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 56%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 14%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 16%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 56%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c [ 56%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 56%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 56%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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-I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 66%] Linking C executable bpm_utest [ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 67%] Built target bpm_utest /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/reproducible-path/kalign-3.4.0/obj-avx' [ 67%] Built target tldevel [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 70%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-avx' [ 70%] 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/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" [ 71%] Linking C executable alphabet_utest [ 71%] Built target edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 72%] Linking C static library libkalign_static.a [ 74%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o 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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g 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-I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 40%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c [ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c [ 40%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 67%] Linking C executable task_utest [ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 67%] Built target task_utest /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/reproducible-path/kalign-3.4.0/obj-avx2' [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 [ 68%] Built target kalign_OBJ [ 68%] Built target tldevel 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/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 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static library libkalign.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script 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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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o 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tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -MF CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o.d -o CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_cmp_test.c [ 85%] Built target kalign_static make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/src /build/reproducible-path/kalign-3.4.0/obj-avx2/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd 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src/CMakeFiles/kalign-bin.dir/run_kalign.c.o [ 89%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP 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/usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 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/build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 [ 98%] Linking CXX executable kaligncpp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Linking C executable dssim [100%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kaligncpp [100%] Built target largebench [100%] Built target dssim [100%] Built target kalign-bin make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_test cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-x86_64-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 Connected to MAKE jobserver test 1 Start 1: bpm_utest 1: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 1: Test timeout computed to be: 1500 test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 2: Test timeout computed to be: 1500 test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 3: Test timeout computed to be: 1500 test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 4: Test timeout computed to be: 1500 test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 10:58:50] : 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: [2026-09-02 10:58:50] : LOG : Check for correctness. 3: [2026-09-02 10:58:50] : LOG : Timing serial 3: [2026-09-02 10:58:50] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 4: 788 155 210 635 401 4: 507 120 774 344 924 4: 889 420 796 445 812 4: 349 560 367 696 303 4: 740 752 448 307 684 4: 809 976 104 100 175 4: 671 356 827 39 217 4: 2 911 832 268 77 4: 385 24 925 582 905 4: 746 562 431 232 797 4: 237 97 712 948 156 4: 72 438 373 175 146 4: 954 318 468 315 221 4: 307 596 927 27 557 4: 410 518 446 166 536 4: 462 637 808 494 542 4: 550 337 980 820 288 4: 662 140 596 231 173 4: 256 291 169 514 793 4: 653 899 664 830 662 4: 808 259 453 369 749 4: 142 313 880 348 356 4: 150 429 82 812 359 4: 817 275 275 616 824 4: 340 777 787 896 831 4: 982 999 204 627 934 4: 945 83 118 284 508 4: 902 448 661 193 62 4: 842 291 732 543 433 4: 55 721 302 143 80 4: 698 573 487 688 884 4: 248 190 441 919 405 4: 142 129 937 999 819 4: 296 495 126 175 117 4: 8 500 318 826 54 4: 11 932 74 499 283 4: 53 340 88 27 386 4: 372 183 756 850 63 4: 480 431 175 918 106 4: 71 386 955 333 577 4: 909 886 343 277 964 4: 151 686 41 779 849 4: 144 877 889 950 157 4: 843 71 311 299 225 4: 821 795 153 327 97 4: 735 808 780 916 462 4: 385 519 483 131 884 4: 939 938 33 984 553 4: 1 412 823 846 159 4: 938 2 247 797 231 4: 49 581 663 670 829 4: 149 684 369 815 524 4: 640 804 513 803 432 4: 618 348 493 82 122 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 6: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Building guide tree. 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Aligning 6: [2026-09-02 10:58:50] : 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 (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 7: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Building guide tree. 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Aligning 7: [2026-09-02 10:58:50] : 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 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 8: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Building guide tree. 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Aligning 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 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 (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 9: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Building guide tree. 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Aligning 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 10: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Building guide tree. 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Aligning 10: [2026-09-02 10:58:50] : 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---- 1/12 Test #2: alphabet_utest ................... Passed 0.02 sec 2/12 Test #3: edist_utest ...................... Passed 0.02 sec 3/12 Test #4: task_utest ....................... Passed 0.02 sec 4/12 Test #5: C++Lib ........................... Passed 0.01 sec 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 11: [2026-09-02 10:58:50] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 12: [2026-09-02 10:58:50] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 10:58:50] : LOG : Protein alignments - 20 seq 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Building guide tree. 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Aligning 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.03 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 10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 10:58:50] : LOG : Testing correctness of AVX bpm. 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% 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: LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2026-09-02 10:59:23] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 37.03 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 37.28 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' set -e ; for SIMD in avx2 avx sse4.1 ; do \ if lscpu | grep -q ${SIMD} ; then \ cd "obj-${SIMD}/" && \ ctest --verbose ; \ cd .. ; \ fi ; \ done UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx2 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/reproducible-path/kalign-3.4.0/obj-avx2/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 10:59:28] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 10:59:28] : 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: [2026-09-02 10:59:34] : LOG : Timing DYN 256 1: [2026-09-02 10:59:36] : LOG : 1.557887 - dyn 1: [2026-09-02 10:59:36] : LOG : 0.056407 - bpm 1: [2026-09-02 10:59:36] : LOG : 0.090412 - bpm_block2 1: [2026-09-02 10:59:36] : LOG : 0.086362 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.59 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 10:59:36] : LOG : Check for correctness. 3: [2026-09-02 10:59:36] : LOG : Timing serial 3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3: [2026-09-02 10:59:36] : LOG : Timing AVX 3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 4: Test timeout computed to be: 1500 4: 696 126 292 831 552 4: 324 318 197 51 270 4: 509 210 42 368 248 4: 516 251 616 292 569 4: 437 824 628 256 850 4: 179 275 732 404 775 4: 807 872 693 869 605 4: 808 558 806 292 991 4: 724 628 609 414 993 4: 299 375 781 741 67 4: 888 149 875 370 10 4: 824 899 623 867 31 4: 886 477 872 40 341 4: 261 137 370 45 893 4: 551 37 190 734 70 4: 458 928 221 190 573 4: 670 274 165 936 452 4: 188 868 292 41 325 4: 997 786 314 427 262 4: 947 398 892 590 507 4: 421 386 79 344 22 4: 838 290 253 359 956 4: 525 565 966 278 56 4: 147 376 273 137 117 4: 24 971 394 918 330 4: 721 845 744 578 679 4: 755 557 536 791 62 4: 83 327 545 631 824 4: 379 165 822 389 588 4: 620 326 649 691 292 4: 140 798 498 483 889 4: 927 913 152 320 427 4: 120 460 244 449 454 4: 592 279 795 561 304 4: 21 271 450 381 577 4: 651 264 302 843 419 4: 868 941 69 508 210 4: 213 776 176 810 851 4: 582 484 807 368 771 4: 539 839 686 140 819 4: 750 657 242 66 510 4: 353 399 31 344 359 4: 442 234 950 166 626 4: 111 261 236 908 216 4: 340 15 546 902 316 4: 654 19 378 380 879 4: 305 807 344 916 904 4: 492 864 81 330 18 4: 963 771 305 547 889 4: 422 627 614 300 389 4: 30 279 691 328 568 4: 248 942 286 120 666 4: 807 907 837 979 149 4: 251 791 532 875 505 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 6: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Building guide tree. 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Aligning 6: [2026-09-02 10:59:36] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 7: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Building guide tree. 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Aligning 7: [2026-09-02 10:59:36] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 8: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Building guide tree. 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Aligning 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 9: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Building guide tree. 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Aligning 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 10: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Building guide tree. 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Aligning 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 11: [2026-09-02 10:59:36] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Building guide tree. 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Aligning 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 10:59:36] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 10:59:36] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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Passed 37.06 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 44.76 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx 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/reproducible-path/kalign-3.4.0/obj-avx/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 11:00:13] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 11:00:13] : 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: [2026-09-02 11:00:19] : LOG : Timing DYN 256 1: [2026-09-02 11:00:20] : LOG : 1.519412 - dyn 1: [2026-09-02 11:00:20] : LOG : 0.000000 - bpm 1: [2026-09-02 11:00:20] : LOG : 0.090842 - bpm_block2 1: [2026-09-02 11:00:20] : LOG : 0.085216 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.18 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 11:00:20] : LOG : Check for correctness. 3: [2026-09-02 11:00:20] : LOG : Timing serial 3: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 4: Test timeout computed to be: 1500 4: 820 299 907 917 4 4: 218 483 485 537 832 4: 316 484 188 840 285 4: 46 764 740 715 473 4: 644 903 694 854 191 4: 972 335 202 485 489 4: 152 490 474 47 535 4: 536 139 402 315 738 4: 148 832 555 372 65 4: 345 861 463 253 401 4: 760 625 235 737 140 4: 739 911 992 192 974 4: 531 635 522 355 431 4: 499 614 92 650 677 4: 177 528 387 122 529 4: 991 679 1 676 489 4: 348 674 61 376 731 4: 596 916 273 859 914 4: 416 533 436 18 338 4: 840 555 775 928 820 4: 611 319 828 23 220 4: 980 994 47 123 524 4: 397 668 111 5 491 4: 424 266 606 271 233 4: 360 676 973 308 107 4: 785 730 62 308 188 4: 681 713 387 797 284 4: 946 705 250 30 161 4: 624 567 993 48 794 4: 519 326 807 720 473 4: 815 241 67 141 517 4: 392 70 52 745 664 4: 431 996 114 736 151 4: 283 841 765 803 676 4: 365 674 971 643 348 4: 405 192 321 126 910 4: 725 320 510 49 556 4: 746 531 139 190 188 4: 260 709 1 926 462 4: 946 225 435 677 276 4: 800 564 212 765 181 4: 487 800 101 499 200 4: 264 994 914 923 241 4: 419 156 891 43 128 4: 3 818 575 240 471 4: 306 9 629 307 893 4: 106 343 548 508 739 4: 129 576 81 636 243 4: 140 30 954 496 58 4: 331 55 13 470 888 4: 588 681 245 234 705 4: 96 179 327 451 132 4: 798 458 922 345 968 4: 130 787 670 989 123 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 6: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Building guide tree. 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Aligning 6: [2026-09-02 11:00:20] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 7: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Building guide tree. 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Aligning 7: [2026-09-02 11:00:20] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 8: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Building guide tree. 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Aligning 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 9: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Building guide tree. 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Aligning 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 10: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Building guide tree. 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Aligning 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 11: [2026-09-02 11:00:20] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Building guide tree. 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Aligning 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 11:00:20] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 11:00:20] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== 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Passed 38.00 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 45.28 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-sse4.1 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/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 11:00:58] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 11:00:59] : 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: [2026-09-02 11:01:04] : LOG : Timing DYN 256 1: [2026-09-02 11:01:06] : LOG : 1.509283 - dyn 1: [2026-09-02 11:01:06] : LOG : 0.000000 - bpm 1: [2026-09-02 11:01:06] : LOG : 0.089574 - bpm_block2 1: [2026-09-02 11:01:06] : LOG : 0.087026 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.20 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 11:01:06] : LOG : Check for correctness. 3: [2026-09-02 11:01:06] : LOG : Timing serial 3: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 4: Test timeout computed to be: 1500 4: 371 637 36 803 652 4: 967 97 417 457 560 4: 25 612 967 128 261 4: 96 913 244 785 705 4: 960 719 649 721 872 4: 294 908 424 678 44 4: 616 88 749 724 890 4: 795 490 997 400 115 4: 110 627 172 215 897 4: 206 85 633 951 294 4: 348 59 790 652 311 4: 272 760 245 633 957 4: 40 871 293 143 669 4: 16 930 888 297 812 4: 638 743 643 585 855 4: 883 226 770 29 271 4: 947 262 54 516 644 4: 46 897 974 289 991 4: 779 697 958 666 968 4: 511 290 872 234 58 4: 36 11 894 71 470 4: 595 154 884 650 849 4: 496 516 109 479 727 4: 888 901 702 626 723 4: 491 175 792 739 66 4: 571 764 816 112 903 4: 493 34 999 368 618 4: 342 80 63 867 379 4: 601 838 866 967 629 4: 548 604 765 488 136 4: 376 878 478 612 584 4: 111 143 339 323 261 4: 139 567 308 283 139 4: 609 49 238 974 603 4: 190 321 259 589 968 4: 893 376 457 904 96 4: 691 411 328 13 783 4: 278 310 367 883 904 4: 951 270 341 914 520 4: 418 156 285 35 964 4: 8 673 804 464 198 4: 684 202 976 742 268 4: 537 501 773 751 327 4: 489 296 864 988 109 4: 620 15 665 101 171 4: 84 810 334 467 843 4: 706 242 32 224 870 4: 576 911 329 899 998 4: 387 78 107 85 719 4: 202 283 615 982 802 4: 93 697 673 793 591 4: 622 923 455 704 367 4: 842 899 289 710 882 4: 939 886 568 512 282 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 6: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Building guide tree. 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Aligning 6: [2026-09-02 11:01:06] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 7: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Building guide tree. 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Aligning 7: [2026-09-02 11:01:06] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 8: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Building guide tree. 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Aligning 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 9: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Building guide tree. 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Aligning 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 10: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Building guide tree. 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Aligning 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 11: [2026-09-02 11:01:06] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Building guide tree. 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Aligning 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.02 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 11:01:06] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 11:01:06] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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Passed 37.09 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 44.46 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/libkalign.a -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign_export.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets-none.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfig.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfigVersion.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin/kalign make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' rm -rf debian/kalign/usr/lib/x86_64-linux-gnu/ dh_install obj-x86_64-linux-gnu/src/kalignfmt usr/bin mkdir -p debian/kalign/usr/lib/kalign/bin cp obj-avx2/src/kalign debian/kalign/usr/lib/kalign/kalign-avx2 cp obj-avx/src/kalign debian/kalign/usr/lib/kalign/kalign-avx cp obj-sse4.1/src/kalign debian/kalign/usr/lib/kalign/kalign-sse4.1 cp obj-avx2/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx2 cp obj-avx/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx cp obj-sse4.1/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-sse4.1 mv debian/kalign/usr/bin/kalign debian/kalign/usr/lib/kalign/kalign-plain mv debian/kalign/usr/bin/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-plain dh_install -pkalign debian/bin/simd-dispatch /usr/lib/kalign/bin cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalign cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalignfmt make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' 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 debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_md5sums dh_builddeb dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.4.0-1_amd64.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.4.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.4.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../kalign_3.4.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1867936 and its subdirectories I: Current time: Tue Sep 1 23:01:51 -12 2026 I: pbuilder-time-stamp: 1788346911 Wed Sep 2 11:01:51 UTC 2026 I: Signing ./b1/kalign_3.4.0-1_amd64.buildinfo as kalign_3.4.0-1_amd64.buildinfo.asc Wed Sep 2 11:01:51 UTC 2026 I: Signed ./b1/kalign_3.4.0-1_amd64.buildinfo as ./b1/kalign_3.4.0-1_amd64.buildinfo.asc Wed Sep 2 11:01:51 UTC 2026 - build #1 for kalign/trixie/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Wed Sep 2 11:01:51 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-q1zpyvmK, removing. /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 04:38 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 04:32 b2 -rw-r--r-- 1 jenkins jenkins 1962 Apr 2 2024 kalign_3.4.0-1.dsc -rw------- 1 jenkins jenkins 3052 Jul 31 04:32 rbuildlog.xYleqpp /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1: total 2676 -rw-r--r-- 1 jenkins jenkins 972166 Jul 31 04:38 build.log -rw-r--r-- 1 jenkins jenkins 674184 Jul 31 04:38 kalign-dbgsym_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12372 Jul 31 04:38 kalign_3.4.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1962 Jul 31 04:38 kalign_3.4.0-1.dsc -rw-r--r-- 1 jenkins jenkins 5888 Jul 31 04:38 kalign_3.4.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6770 Jul 31 04:38 kalign_3.4.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1380 Jul 31 04:38 kalign_3.4.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 137544 Jul 31 04:38 kalign_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1495 Jul 31 04:38 kalign_3.4.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 903277 Jul 31 04:38 kalign_3.4.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2: total 0 Thu Jul 31 04:38:52 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 1 22:55:51 -12 2026 I: pbuilder-time-stamp: 1788346551 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kalign_3.4.0-1.dsc] I: copying [./kalign_3.4.0.orig.tar.gz] I: copying [./kalign_3.4.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./kalign_3.4.0-1.dsc: no acceptable signature found dpkg-source: info: extracting kalign in kalign-3.4.0 dpkg-source: info: unpacking kalign_3.4.0.orig.tar.gz dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8fee02fc933e4602b39349a6300fdb23' 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='1867936' 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.u98MuRLQ/pbuilderrc_uT3F --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-8 [881 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b2 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 31.9 MB in 6s (5250 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-8_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-8_amd64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../18-cmake-data_3.31.6-2_all.deb ... Unpacking cmake-data (3.31.6-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../19-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../20-libarchive13t64_3.7.4-4_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../36-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../37-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../38-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../39-libgnutls30t64_3.8.9-3_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../41-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../42-libcurl4t64_8.14.1-2_amd64.deb ... Unpacking libcurl4t64:amd64 (8.14.1-2) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../43-libjsoncpp26_1.9.6-3_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-3) ... Selecting previously unselected package librhash1:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/kalign-3.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kalign_3.4.0-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.4.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/reproducible-path/kalign-3.4.0' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (4.7s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-sse4.1 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-sse4.1 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (9.3s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-sse4.1 dh_auto_configure --builddirectory obj-avx -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF cd obj-avx && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (11.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx dh_auto_configure --builddirectory obj-avx2 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON cd obj-avx2 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- Performing Test HAVE_AVX2 -- Performing Test HAVE_AVX2 - Success -- AVX2 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (7.9s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx2 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 10%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 14%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 14%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 16%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 17%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 21%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c [ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 24%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 27%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 33%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 41%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC 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/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 66%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 [ 67%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 68%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 68%] Built target task_utest [ 68%] Built target bpm_utest [ 70%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 [ 70%] 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[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 71%] Linking C static library libkalign.a [ 72%] Linking C static library libkalign_static.a [ 72%] Built target alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake [ 72%] Built target edist_utest cd 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"--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests 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src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd 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make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f 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lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 13%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 14%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 17%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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-DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 20%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 21%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 22%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 28%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 29%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 27%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c [ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 64%] 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/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 67%] Linking C static library libkalign_static.a [ 67%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 [ 70%] Linking C executable task_utest [ 71%] Linking C executable alphabet_utest [ 72%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 74%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' /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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign_static.a /usr/bin/ar qc libkalign.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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 74%] Built target edist_utest /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d CMakeFiles/task_utest.dir/src/tldevel.c.o CMakeFiles/task_utest.dir/src/tlrng.c.o 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kalign_cmp_test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kaligncpp.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -MF CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o.d -o CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_io_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/c++ -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -MF 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" [ 83%] Building C object tests/CMakeFiles/dssim.dir/dssim_test.c.o [ 82%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o [ 83%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim_test.c.o -MF CMakeFiles/dssim.dir/dssim_test.c.o.d -o CMakeFiles/dssim.dir/dssim_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim_test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c [ 86%] Building C object src/CMakeFiles/kalign-bin.dir/parameters.c.o [ 86%] Linking C executable kalign_cmp_test cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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src/CMakeFiles/kalignfmt.dir/run_reformat.c.o [ 93%] Linking C executable kalign_io_test [ 93%] Building C object src/CMakeFiles/kalignfmt.dir/parameters.c.o [ 91%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/run_reformat.c.o -MF CMakeFiles/kalignfmt.dir/run_reformat.c.o.d -o CMakeFiles/kalignfmt.dir/run_reformat.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_reformat.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/largebench.dir/large_benchmark.c.o -MF CMakeFiles/largebench.dir/large_benchmark.c.o.d -o CMakeFiles/largebench.dir/large_benchmark.c.o -c /build/reproducible-path/kalign-3.4.0/tests/large_benchmark.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration 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"GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 98%] Built target kalign-bin /usr/bin/cc -g -O2 -Werror=implicit-function-declaration 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 18%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 20%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 22%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c [ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 12%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 56%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 56%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 56%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 14%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 16%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 56%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c [ 56%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 56%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 56%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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/build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 66%] Linking C executable bpm_utest [ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P 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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/reproducible-path/kalign-3.4.0/obj-avx' [ 67%] Built target tldevel [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 70%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-avx' [ 70%] 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/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 72%] Linking C static library libkalign_static.a [ 74%] Linking C static library libkalign.a cd 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CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a make[4]: Leaving directory 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make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/src /build/reproducible-path/kalign-3.4.0/obj-avx/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/tests 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/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking C executable largebench [ 97%] Built target kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 97%] Built target kalign-bin /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 98%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 [ 98%] Built target largebench /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [100%] Linking C executable dssim cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 [100%] Built target kaligncpp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [100%] Built target dssim make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' dh_auto_build --builddirectory obj-avx2 cd obj-avx2 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-avx2//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 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/build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 18%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 18%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 18%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 21%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 22%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 29%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o [ 31%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o [ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 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-I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 40%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c [ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c [ 40%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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_seqprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 67%] Linking C executable task_utest [ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 67%] Built target task_utest /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/reproducible-path/kalign-3.4.0/obj-avx2' [ 68%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 [ 68%] Built target kalign_OBJ [ 68%] Built target tldevel 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/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 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static library libkalign.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script 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tests/CMakeFiles/dssim.dir/dssim.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -MF CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o.d -o CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include 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-I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -MF CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o.d -o CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_cmp_test.c [ 85%] Built target kalign_static make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/src /build/reproducible-path/kalign-3.4.0/obj-avx2/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/tests /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/build make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 87%] Building C object src/CMakeFiles/kalign-bin.dir/parameters.c.o [ 87%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o [ 89%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/largebench.dir/large_benchmark.c.o -MF CMakeFiles/largebench.dir/large_benchmark.c.o.d -o CMakeFiles/largebench.dir/large_benchmark.c.o -c /build/reproducible-path/kalign-3.4.0/tests/large_benchmark.c [ 90%] Linking C executable kalign_io_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 [ 93%] Linking C executable kalign_lib_test [ 93%] Linking C executable kalign_cmp_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 94%] Linking C executable kalign [ 95%] Linking C executable kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 [ 95%] Built target kalign_cmp_test [ 95%] Built target kalign_io_test [ 95%] Built target kalign_lib_test [ 97%] Linking C executable largebench cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 [ 98%] Linking CXX executable kaligncpp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Linking C executable dssim [100%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kaligncpp [100%] Built target largebench [100%] Built target dssim [100%] Built target kalign-bin make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_test cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-x86_64-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 Connected to MAKE jobserver test 1 Start 1: bpm_utest 1: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 1: Test timeout computed to be: 1500 test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 2: Test timeout computed to be: 1500 test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 3: Test timeout computed to be: 1500 test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 4: Test timeout computed to be: 1500 test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 10:58:50] : 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: [2026-09-02 10:58:50] : LOG : Check for correctness. 3: [2026-09-02 10:58:50] : LOG : Timing serial 3: [2026-09-02 10:58:50] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 4: 788 155 210 635 401 4: 507 120 774 344 924 4: 889 420 796 445 812 4: 349 560 367 696 303 4: 740 752 448 307 684 4: 809 976 104 100 175 4: 671 356 827 39 217 4: 2 911 832 268 77 4: 385 24 925 582 905 4: 746 562 431 232 797 4: 237 97 712 948 156 4: 72 438 373 175 146 4: 954 318 468 315 221 4: 307 596 927 27 557 4: 410 518 446 166 536 4: 462 637 808 494 542 4: 550 337 980 820 288 4: 662 140 596 231 173 4: 256 291 169 514 793 4: 653 899 664 830 662 4: 808 259 453 369 749 4: 142 313 880 348 356 4: 150 429 82 812 359 4: 817 275 275 616 824 4: 340 777 787 896 831 4: 982 999 204 627 934 4: 945 83 118 284 508 4: 902 448 661 193 62 4: 842 291 732 543 433 4: 55 721 302 143 80 4: 698 573 487 688 884 4: 248 190 441 919 405 4: 142 129 937 999 819 4: 296 495 126 175 117 4: 8 500 318 826 54 4: 11 932 74 499 283 4: 53 340 88 27 386 4: 372 183 756 850 63 4: 480 431 175 918 106 4: 71 386 955 333 577 4: 909 886 343 277 964 4: 151 686 41 779 849 4: 144 877 889 950 157 4: 843 71 311 299 225 4: 821 795 153 327 97 4: 735 808 780 916 462 4: 385 519 483 131 884 4: 939 938 33 984 553 4: 1 412 823 846 159 4: 938 2 247 797 231 4: 49 581 663 670 829 4: 149 684 369 815 524 4: 640 804 513 803 432 4: 618 348 493 82 122 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 6: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Building guide tree. 6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:58:50] : LOG : Aligning 6: [2026-09-02 10:58:50] : 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 (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 7: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Building guide tree. 7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:58:50] : LOG : Aligning 7: [2026-09-02 10:58:50] : 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 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 8: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Building guide tree. 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:58:50] : LOG : Aligning 8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 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 (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 9: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Building guide tree. 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:58:50] : LOG : Aligning 9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 10: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Building guide tree. 10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:58:50] : LOG : Aligning 10: [2026-09-02 10:58:50] : 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---- 1/12 Test #2: alphabet_utest ................... Passed 0.02 sec 2/12 Test #3: edist_utest ...................... Passed 0.02 sec 3/12 Test #4: task_utest ....................... Passed 0.02 sec 4/12 Test #5: C++Lib ........................... Passed 0.01 sec 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:58:50] : LOG : Detected protein sequences. 11: [2026-09-02 10:58:50] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances 12: [2026-09-02 10:58:50] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 10:58:50] : LOG : Protein alignments - 20 seq 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Building guide tree. 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: [2026-09-02 10:58:50] : LOG : Aligning 11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.03 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 10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 10:58:50] : LOG : Testing correctness of AVX bpm. 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% 12: [2026-09-02 10:58:53] : LOG : Protein alignments - 1000 seq 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: [2026-09-02 10:58:55] : LOG : Timing DYN 256 1: [2026-09-02 10:58:57] : LOG : 1.557818 - dyn 1: [2026-09-02 10:58:57] : LOG : 0.000000 - bpm 1: [2026-09-02 10:58:57] : LOG : 0.089773 - bpm_block2 1: [2026-09-02 10:58:57] : LOG : 0.085551 - bpm_block 11/12 Test #1: bpm_utest ........................ Passed 7.19 sec 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2026-09-02 10:59:05] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12: [2026-09-02 10:59:14] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 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: LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2026-09-02 10:59:23] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 37.03 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 37.28 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' set -e ; for SIMD in avx2 avx sse4.1 ; do \ if lscpu | grep -q ${SIMD} ; then \ cd "obj-${SIMD}/" && \ ctest --verbose ; \ cd .. ; \ fi ; \ done UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx2 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/reproducible-path/kalign-3.4.0/obj-avx2/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 10:59:28] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 10:59:28] : 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: [2026-09-02 10:59:34] : LOG : Timing DYN 256 1: [2026-09-02 10:59:36] : LOG : 1.557887 - dyn 1: [2026-09-02 10:59:36] : LOG : 0.056407 - bpm 1: [2026-09-02 10:59:36] : LOG : 0.090412 - bpm_block2 1: [2026-09-02 10:59:36] : LOG : 0.086362 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.59 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 10:59:36] : LOG : Check for correctness. 3: [2026-09-02 10:59:36] : LOG : Timing serial 3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3: [2026-09-02 10:59:36] : LOG : Timing AVX 3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 4: Test timeout computed to be: 1500 4: 696 126 292 831 552 4: 324 318 197 51 270 4: 509 210 42 368 248 4: 516 251 616 292 569 4: 437 824 628 256 850 4: 179 275 732 404 775 4: 807 872 693 869 605 4: 808 558 806 292 991 4: 724 628 609 414 993 4: 299 375 781 741 67 4: 888 149 875 370 10 4: 824 899 623 867 31 4: 886 477 872 40 341 4: 261 137 370 45 893 4: 551 37 190 734 70 4: 458 928 221 190 573 4: 670 274 165 936 452 4: 188 868 292 41 325 4: 997 786 314 427 262 4: 947 398 892 590 507 4: 421 386 79 344 22 4: 838 290 253 359 956 4: 525 565 966 278 56 4: 147 376 273 137 117 4: 24 971 394 918 330 4: 721 845 744 578 679 4: 755 557 536 791 62 4: 83 327 545 631 824 4: 379 165 822 389 588 4: 620 326 649 691 292 4: 140 798 498 483 889 4: 927 913 152 320 427 4: 120 460 244 449 454 4: 592 279 795 561 304 4: 21 271 450 381 577 4: 651 264 302 843 419 4: 868 941 69 508 210 4: 213 776 176 810 851 4: 582 484 807 368 771 4: 539 839 686 140 819 4: 750 657 242 66 510 4: 353 399 31 344 359 4: 442 234 950 166 626 4: 111 261 236 908 216 4: 340 15 546 902 316 4: 654 19 378 380 879 4: 305 807 344 916 904 4: 492 864 81 330 18 4: 963 771 305 547 889 4: 422 627 614 300 389 4: 30 279 691 328 568 4: 248 942 286 120 666 4: 807 907 837 979 149 4: 251 791 532 875 505 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 6: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Building guide tree. 6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 10:59:36] : LOG : Aligning 6: [2026-09-02 10:59:36] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 7: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Building guide tree. 7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 10:59:36] : LOG : Aligning 7: [2026-09-02 10:59:36] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 8: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Building guide tree. 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 10:59:36] : LOG : Aligning 8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 9: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Building guide tree. 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 10:59:36] : LOG : Aligning 9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 10: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Building guide tree. 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 10:59:36] : LOG : Aligning 10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 10:59:36] : LOG : Detected protein sequences. 11: [2026-09-02 10:59:36] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Building guide tree. 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 10:59:36] : LOG : Aligning 11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 10:59:36] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 10:59:36] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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Passed 37.06 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 44.76 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx 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/reproducible-path/kalign-3.4.0/obj-avx/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 11:00:13] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 11:00:13] : 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: [2026-09-02 11:00:19] : LOG : Timing DYN 256 1: [2026-09-02 11:00:20] : LOG : 1.519412 - dyn 1: [2026-09-02 11:00:20] : LOG : 0.000000 - bpm 1: [2026-09-02 11:00:20] : LOG : 0.090842 - bpm_block2 1: [2026-09-02 11:00:20] : LOG : 0.085216 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.18 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 11:00:20] : LOG : Check for correctness. 3: [2026-09-02 11:00:20] : LOG : Timing serial 3: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 4: Test timeout computed to be: 1500 4: 820 299 907 917 4 4: 218 483 485 537 832 4: 316 484 188 840 285 4: 46 764 740 715 473 4: 644 903 694 854 191 4: 972 335 202 485 489 4: 152 490 474 47 535 4: 536 139 402 315 738 4: 148 832 555 372 65 4: 345 861 463 253 401 4: 760 625 235 737 140 4: 739 911 992 192 974 4: 531 635 522 355 431 4: 499 614 92 650 677 4: 177 528 387 122 529 4: 991 679 1 676 489 4: 348 674 61 376 731 4: 596 916 273 859 914 4: 416 533 436 18 338 4: 840 555 775 928 820 4: 611 319 828 23 220 4: 980 994 47 123 524 4: 397 668 111 5 491 4: 424 266 606 271 233 4: 360 676 973 308 107 4: 785 730 62 308 188 4: 681 713 387 797 284 4: 946 705 250 30 161 4: 624 567 993 48 794 4: 519 326 807 720 473 4: 815 241 67 141 517 4: 392 70 52 745 664 4: 431 996 114 736 151 4: 283 841 765 803 676 4: 365 674 971 643 348 4: 405 192 321 126 910 4: 725 320 510 49 556 4: 746 531 139 190 188 4: 260 709 1 926 462 4: 946 225 435 677 276 4: 800 564 212 765 181 4: 487 800 101 499 200 4: 264 994 914 923 241 4: 419 156 891 43 128 4: 3 818 575 240 471 4: 306 9 629 307 893 4: 106 343 548 508 739 4: 129 576 81 636 243 4: 140 30 954 496 58 4: 331 55 13 470 888 4: 588 681 245 234 705 4: 96 179 327 451 132 4: 798 458 922 345 968 4: 130 787 670 989 123 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 6: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Building guide tree. 6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:00:20] : LOG : Aligning 6: [2026-09-02 11:00:20] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 7: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Building guide tree. 7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:00:20] : LOG : Aligning 7: [2026-09-02 11:00:20] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 8: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Building guide tree. 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:00:20] : LOG : Aligning 8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 9: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Building guide tree. 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:00:20] : LOG : Aligning 9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 10: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Building guide tree. 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:00:20] : LOG : Aligning 10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:00:20] : LOG : Detected protein sequences. 11: [2026-09-02 11:00:20] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Building guide tree. 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 11:00:20] : LOG : Aligning 11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 11:00:20] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 11:00:20] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== 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Passed 38.00 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 45.28 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-sse4.1 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/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2026-09-02 11:00:58] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2026-09-02 11:00:59] : 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: [2026-09-02 11:01:04] : LOG : Timing DYN 256 1: [2026-09-02 11:01:06] : LOG : 1.509283 - dyn 1: [2026-09-02 11:01:06] : LOG : 0.000000 - bpm 1: [2026-09-02 11:01:06] : LOG : 0.089574 - bpm_block2 1: [2026-09-02 11:01:06] : LOG : 0.087026 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.20 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 3: Test timeout computed to be: 1500 3: [2026-09-02 11:01:06] : LOG : Check for correctness. 3: [2026-09-02 11:01:06] : LOG : Timing serial 3: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 4: Test timeout computed to be: 1500 4: 371 637 36 803 652 4: 967 97 417 457 560 4: 25 612 967 128 261 4: 96 913 244 785 705 4: 960 719 649 721 872 4: 294 908 424 678 44 4: 616 88 749 724 890 4: 795 490 997 400 115 4: 110 627 172 215 897 4: 206 85 633 951 294 4: 348 59 790 652 311 4: 272 760 245 633 957 4: 40 871 293 143 669 4: 16 930 888 297 812 4: 638 743 643 585 855 4: 883 226 770 29 271 4: 947 262 54 516 644 4: 46 897 974 289 991 4: 779 697 958 666 968 4: 511 290 872 234 58 4: 36 11 894 71 470 4: 595 154 884 650 849 4: 496 516 109 479 727 4: 888 901 702 626 723 4: 491 175 792 739 66 4: 571 764 816 112 903 4: 493 34 999 368 618 4: 342 80 63 867 379 4: 601 838 866 967 629 4: 548 604 765 488 136 4: 376 878 478 612 584 4: 111 143 339 323 261 4: 139 567 308 283 139 4: 609 49 238 974 603 4: 190 321 259 589 968 4: 893 376 457 904 96 4: 691 411 328 13 783 4: 278 310 367 883 904 4: 951 270 341 914 520 4: 418 156 285 35 964 4: 8 673 804 464 198 4: 684 202 976 742 268 4: 537 501 773 751 327 4: 489 296 864 988 109 4: 620 15 665 101 171 4: 84 810 334 467 843 4: 706 242 32 224 870 4: 576 911 329 899 998 4: 387 78 107 85 719 4: 202 283 615 982 802 4: 93 697 673 793 591 4: 622 923 455 704 367 4: 842 899 289 710 882 4: 939 886 568 512 282 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 6: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Building guide tree. 6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2026-09-02 11:01:06] : LOG : Aligning 6: [2026-09-02 11:01:06] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 7: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Building guide tree. 7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2026-09-02 11:01:06] : LOG : Aligning 7: [2026-09-02 11:01:06] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 8: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Building guide tree. 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2026-09-02 11:01:06] : LOG : Aligning 8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 9: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Building guide tree. 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2026-09-02 11:01:06] : LOG : Aligning 9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 10: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Building guide tree. 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2026-09-02 11:01:06] : LOG : Aligning 10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2026-09-02 11:01:06] : LOG : Detected protein sequences. 11: [2026-09-02 11:01:06] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Building guide tree. 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2026-09-02 11:01:06] : LOG : Aligning 11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.02 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2026-09-02 11:01:06] : LOG : DSSim - a simplistic sequence simulator. 12: [2026-09-02 11:01:06] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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Passed 37.09 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 44.46 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/libkalign.a -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign_export.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets-none.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfig.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfigVersion.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin/kalign make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' rm -rf debian/kalign/usr/lib/x86_64-linux-gnu/ dh_install obj-x86_64-linux-gnu/src/kalignfmt usr/bin mkdir -p debian/kalign/usr/lib/kalign/bin cp obj-avx2/src/kalign debian/kalign/usr/lib/kalign/kalign-avx2 cp obj-avx/src/kalign debian/kalign/usr/lib/kalign/kalign-avx cp obj-sse4.1/src/kalign debian/kalign/usr/lib/kalign/kalign-sse4.1 cp obj-avx2/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx2 cp obj-avx/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx cp obj-sse4.1/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-sse4.1 mv debian/kalign/usr/bin/kalign debian/kalign/usr/lib/kalign/kalign-plain mv debian/kalign/usr/bin/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-plain dh_install -pkalign debian/bin/simd-dispatch /usr/lib/kalign/bin cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalign cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalignfmt make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' 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 debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_md5sums dh_builddeb dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.4.0-1_amd64.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.4.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.4.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../kalign_3.4.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1867936 and its subdirectories I: Current time: Tue Sep 1 23:01:51 -12 2026 I: pbuilder-time-stamp: 1788346911 Thu Jul 31 04:38:52 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Jul 31 04:38:52 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Jul 31 04:38:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Jul 31 04:38:52 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-P550db' ==================================================================================== Thu Jul 31 04:38:53 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 kalign trixie /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ 1:3.4.0-1" as arguments. Thu Jul 31 04:38:53 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-IMw798F0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 04:38:53 UTC 2025 I: Downloading source for trixie/kalign=1:3.4.0-1 Reading package lists... NOTICE: 'kalign' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kalign.git Please use: git clone https://salsa.debian.org/med-team/kalign.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 918 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (dsc) [1962 B] Get:2 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (tar) [903 kB] Get:3 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (diff) [12.4 kB] Fetched 918 kB in 0s (37.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'kalign' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kalign.git Please use: git clone https://salsa.debian.org/med-team/kalign.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 918 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (dsc) [1962 B] Get:2 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (tar) [903 kB] Get:3 http://deb.debian.org/debian trixie/main kalign 1:3.4.0-1 (diff) [12.4 kB] Fetched 918 kB in 0s (37.2 MB/s) Download complete and in download only mode ============================================================================= Re-Building kalign in trixie on amd64 on ionos11-amd64 now. Date: Thu Jul 31 04:38:53 UTC 2025 Date UTC: Thu Jul 31 04:38:53 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/pbuilderrc_ZF1P + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' kalign = debian-installer -o kalign = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' kalign = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/pbuilderrc_ZF1P --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2 --logfile b2/build.log kalign_3.4.0-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 31 18:38:54 +14 2025 I: pbuilder-time-stamp: 1753936734 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kalign_3.4.0-1.dsc] I: copying [./kalign_3.4.0.orig.tar.gz] I: copying [./kalign_3.4.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./kalign_3.4.0-1.dsc: no acceptable signature found dpkg-source: info: extracting kalign in kalign-3.4.0 dpkg-source: info: unpacking kalign_3.4.0.orig.tar.gz dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 31 04:39 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=511f0f45f685463fa5b8ae9d39cb16b6 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2208375 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/pbuilderrc_ZF1P --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2 --logfile b2/build.log kalign_3.4.0-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-8 [881 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-4 [349 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b2 [25.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 31.9 MB in 3s (9365 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-8_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-8) ... Selecting previously unselected package procps. 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Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. 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Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../36-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../37-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../38-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../39-libgnutls30t64_3.8.9-3_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../41-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../42-libcurl4t64_8.14.1-2_amd64.deb ... Unpacking libcurl4t64:amd64 (8.14.1-2) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../43-libjsoncpp26_1.9.6-3_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-3) ... Selecting previously unselected package librhash1:amd64. 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Preparing to unpack .../56-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../57-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../58-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../59-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libcom-err2:amd64 (1.47.2-3+b2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-8) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up cmake-data (3.31.6-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libarchive13t64:amd64 (3.7.4-4) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up debhelper (13.24.2) ... Setting up cmake (3.31.6-2) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/kalign-3.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kalign_3.4.0-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.4.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/reproducible-path/kalign-3.4.0' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=OFF -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (1.4s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-sse4.1 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF cd obj-sse4.1 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=OFF -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (1.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-sse4.1 dh_auto_configure --builddirectory obj-avx -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF cd obj-avx && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=OFF .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (2.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx dh_auto_configure --builddirectory obj-avx2 -- -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON cd obj-avx2 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DINSTALL_PREFIX=/usr -DENABLE_SSE=ON -DENABLE_AVX=ON -DENABLE_AVX2=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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. -- Performing Test HAVE_SSE -- Performing Test HAVE_SSE - Success -- SSE4.1 is enabled - target CPU must support it -- Performing Test HAVE_AVX -- Performing Test HAVE_AVX - Success -- AVX is enabled - target CPU must support it -- Performing Test HAVE_AVX2 -- Performing Test HAVE_AVX2 - Success -- AVX2 is enabled - target CPU must support it -- 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp -- Configuring done (4.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx2 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 12%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 16%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o [ 16%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 18%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 22%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 28%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o [ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 33%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 13%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 41%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 41%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 41%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c [ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 66%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 67%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 [ 68%] Linking C static library libtldevel.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 68%] Built target alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 70%] Linking C executable task_utest /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 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 70%] 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[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 70%] Built target tldevel make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 70%] Built target bpm_utest [ 71%] Linking C static library libkalign_static.a [ 72%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake [ 74%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake 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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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a /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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign_static.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 74%] Built target edist_utest [ 74%] Built target kalign make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend [ 74%] Built target kalign_static make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/kalign_io_test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests 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/build/reproducible-path/kalign-3.4.0/tests/dssim.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -MF CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o.d -o CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_cmp_test.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 93%] Linking C executable kalign_cmp_test [ 93%] Linking C executable kalign [ 93%] Linking C executable kalign_io_test cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 [ 94%] Linking C executable kalign_lib_test [ 95%] Linking C executable kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 2%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 4%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 5%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 5%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c make[4]: Leaving 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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'/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 12%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 12%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o [ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 13%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 14%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 18%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 18%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o [ 20%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 20%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 27%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 28%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 28%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c [ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o [ 33%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC 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lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 66%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 66%] Built target kalign_OBJ make -f 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/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 74%] Built target kalign [ 74%] Built target task_utest [ 74%] Built target edist_utest [ 74%] Built target tldevel [ 74%] Built target bpm_utest /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 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/build/reproducible-path/kalign-3.4.0/src/run_kalign.c [ 91%] Linking C executable kalign_cmp_test [ 91%] Linking C executable kalign_io_test cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 91%] Built target kalign_cmp_test [ 91%] Built target kalign_io_test [ 93%] Linking C executable kalign_lib_test [ 94%] Linking C executable kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' [ 94%] Built target kalignfmt [ 94%] Built target kalign_lib_test [ 98%] Linking C executable dssim [ 98%] Linking C executable largebench [ 98%] Linking C executable kalign cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 [100%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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'/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 2%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 4%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o [ 5%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o [ 8%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o [ 9%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 10%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 10%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o [ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o [ 13%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 43%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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/build/reproducible-path/kalign-3.4.0/lib/src/bpm.c [ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 51%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o [ 51%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o [ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 51%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 51%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o [ 51%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 51%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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-I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 66%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 [ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /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 [ 70%] Linking C executable edist_utest [ 70%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 71%] Built target bpm_utest [ 71%] Linking C executable task_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 [ 71%] 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/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" [ 71%] Built target tldevel make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 72%] Linking C static library libkalign.a [ 74%] Linking C static library libkalign_static.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [ 74%] Built target alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 [ 74%] Built target edist_utest [ 74%] Built target task_utest /usr/bin/ar qc libkalign.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 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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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o 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cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/src /build/reproducible-path/kalign-3.4.0/obj-avx/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/tests /build/reproducible-path/kalign-3.4.0/obj-avx/tests/CMakeFiles/kalign_io_test.dir/DependInfo.cmake "--color=" make[4]: Entering directory 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"--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/src /build/reproducible-path/kalign-3.4.0/obj-avx/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/tests /build/reproducible-path/kalign-3.4.0/obj-avx/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/build make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/build make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory 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object src/CMakeFiles/kalignfmt.dir/run_reformat.c.o [ 78%] Building C object src/CMakeFiles/kalignfmt.dir/parameters.c.o [ 81%] Building C object tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o [ 81%] Building C object tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o [ 82%] Building CXX object tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/run_reformat.c.o -MF 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-I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c [ 87%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o [ 87%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o [ 87%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cc -DHAVE_OPENMP 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^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | 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'/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o [ 9%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o [ 9%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o [ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o [ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o [ 10%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o [ 12%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o [ 13%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o [ 14%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o [ 17%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o [ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c [ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o [ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o [ 31%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c [ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o [ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o [ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o [ 32%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o [ 32%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 32%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c [ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o [ 36%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c [ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o [ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o [ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c [ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o [ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 66%] Linking C executable edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 [ 67%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 67%] 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/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 70%] Linking C static library libkalign.a [ 70%] Linking C static library libkalign_static.a [ 70%] Built target alphabet_utest [ 70%] Built target edist_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 [ 74%] Linking C executable task_utest [ 72%] Linking C static library libtldevel.a [ 74%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 74%] Built target task_utest [ 74%] Built target bpm_utest /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/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/ar qc libkalign.a CMakeFiles/kalign_OBJ.dir/src/test.c.o 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-Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c [ 90%] Linking C executable kalign_io_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 [ 91%] Linking C executable kalign_cmp_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 [ 93%] Built target kalign_io_test [ 93%] Built target kalign_cmp_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [ 93%] Built target kalign_lib_test /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Linking C executable kalign [ 95%] Linking C executable kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 [ 97%] Linking C executable largebench cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 [ 98%] Linking C executable dssim cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 [100%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a [100%] Built target largebench make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kalign-bin [100%] Built target dssim /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kaligncpp make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_test cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-x86_64-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 Connected to MAKE jobserver test 1 Start 1: bpm_utest 1: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 1: Test timeout computed to be: 1500 test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 2: Test timeout computed to be: 1500 test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 3: Test timeout computed to be: 1500 test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib 4: Test timeout computed to be: 1500 test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 1: [2025-07-31 04:39:47] : 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: [2025-07-31 04:39:47] : LOG : Check for correctness. 3: [2025-07-31 04:39:47] : LOG : Timing serial 3: [2025-07-31 04:39:47] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 4: 176 596 917 495 951 4: 889 193 524 787 661 4: 691 561 765 759 771 4: 227 623 645 750 227 4: 714 679 372 198 377 4: 973 651 59 655 15 4: 64 224 236 305 396 4: 952 450 6 843 587 4: 122 147 580 234 558 4: 346 419 672 553 649 4: 678 753 661 51 279 4: 616 946 108 439 435 4: 622 881 219 965 450 4: 955 872 208 51 69 4: 15 81 296 184 311 4: 381 702 189 139 128 4: 703 61 745 472 195 4: 980 134 119 684 305 4: 350 212 497 613 729 4: 257 855 608 390 839 4: 990 854 160 798 579 4: 948 738 922 542 25 4: 289 107 38 558 275 4: 698 366 107 413 333 4: 235 237 21 691 313 4: 1 798 917 296 30 4: 304 124 759 758 852 4: 463 994 444 990 177 4: 919 719 988 280 50 4: 202 238 469 782 948 4: 207 462 919 195 882 4: 950 877 519 736 134 4: 911 757 247 123 287 4: 617 285 231 444 748 4: 531 547 690 800 590 4: 714 224 496 235 397 4: 818 548 877 52 460 4: 269 943 592 461 597 4: 548 616 302 621 388 4: 254 676 353 107 648 4: 408 675 588 832 7 4: 355 133 123 486 754 4: 934 410 166 654 139 4: 562 37 555 636 429 4: 582 483 383 822 634 4: 44 161 697 306 228 4: 590 97 620 696 645 4: 222 622 120 126 386 4: 553 750 419 805 585 4: 5 625 556 748 227 4: 147 644 348 43 903 4: 305 68 330 7 249 4: 463 185 707 640 869 4: 806 491 371 350 404 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 6: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:39:47] : LOG : Building guide tree. 6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:39:47] : LOG : Aligning 6: [2025-07-31 04:39:47] : 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 (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 7: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:39:47] : LOG : Building guide tree. 7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:39:47] : LOG : Aligning 7: [2025-07-31 04:39:47] : 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 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 8: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:39:47] : LOG : Building guide tree. 8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:39:47] : LOG : Aligning 8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 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 (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 9: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:39:47] : LOG : Building guide tree. 9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:39:47] : LOG : Aligning 9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.01u 00:00:00.00 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---- 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 10: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:39:47] : LOG : Building guide tree. 10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:39:47] : LOG : Aligning 10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 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---- 1/12 Test #2: alphabet_utest ................... Passed 0.02 sec 2/12 Test #3: edist_utest ...................... Passed 0.01 sec 3/12 Test #4: task_utest ....................... Passed 0.01 sec 4/12 Test #5: C++Lib ........................... Passed 0.01 sec 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:39:47] : LOG : Detected protein sequences. 11: [2025-07-31 04:39:47] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances 12: [2025-07-31 04:39:47] : LOG : DSSim - a simplistic sequence simulator. 12: [2025-07-31 04:39:47] : LOG : Protein alignments - 20 seq 11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 11: [2025-07-31 04:39:47] : LOG : Building guide tree. 11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: [2025-07-31 04:39:47] : LOG : Aligning 11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.03u 00:00:00.03 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 10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2025-07-31 04:39:47] : LOG : Testing correctness of AVX bpm. 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% 12: [2025-07-31 04:39:51] : LOG : Protein alignments - 1000 seq 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: [2025-07-31 04:39:53] : LOG : Timing DYN 256 1: [2025-07-31 04:39:54] : LOG : 1.480885 - dyn 1: [2025-07-31 04:39:54] : LOG : 0.000000 - bpm 1: [2025-07-31 04:39:54] : LOG : 0.090882 - bpm_block2 1: [2025-07-31 04:39:54] : LOG : 0.085667 - bpm_block 11/12 Test #1: bpm_utest ........................ 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: LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2025-07-31 04:40:20] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.06 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 36.08 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' set -e ; for SIMD in avx2 avx sse4.1 ; do \ if lscpu | grep -q ${SIMD} ; then \ cd "obj-${SIMD}/" && \ ctest --verbose ; \ cd .. ; \ fi ; \ done UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx2 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/reproducible-path/kalign-3.4.0/obj-avx2/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2025-07-31 04:40:24] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2025-07-31 04:40:24] : 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: [2025-07-31 04:40:30] : LOG : Timing DYN 256 1: [2025-07-31 04:40:32] : LOG : 1.512778 - dyn 1: [2025-07-31 04:40:32] : LOG : 0.058957 - bpm 1: [2025-07-31 04:40:32] : LOG : 0.090890 - bpm_block2 1: [2025-07-31 04:40:32] : LOG : 0.084968 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.36 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 3: Test timeout computed to be: 1500 3: [2025-07-31 04:40:32] : LOG : Check for correctness. 3: [2025-07-31 04:40:32] : LOG : Timing serial 3: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3: [2025-07-31 04:40:32] : LOG : Timing AVX 3: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 4: Test timeout computed to be: 1500 4: 854 498 246 170 313 4: 619 617 81 150 721 4: 322 616 867 187 651 4: 238 622 83 186 29 4: 602 202 883 957 346 4: 124 884 557 497 137 4: 504 414 926 632 651 4: 423 382 251 145 300 4: 527 341 740 75 286 4: 530 451 241 166 557 4: 585 767 756 422 550 4: 508 528 913 455 27 4: 912 971 262 294 329 4: 50 387 988 176 855 4: 133 571 295 702 859 4: 950 767 98 393 789 4: 582 482 355 25 460 4: 753 356 885 276 605 4: 44 78 452 979 995 4: 631 446 886 446 366 4: 681 844 865 143 474 4: 4 758 560 817 405 4: 665 981 405 132 163 4: 353 718 848 965 318 4: 357 333 956 189 542 4: 334 687 809 800 493 4: 233 387 720 453 610 4: 800 867 181 766 276 4: 283 227 413 965 178 4: 520 350 251 521 603 4: 194 20 458 382 184 4: 617 46 901 946 488 4: 483 722 120 55 291 4: 494 956 970 102 904 4: 437 340 75 386 789 4: 72 810 854 511 507 4: 666 349 801 882 806 4: 415 353 771 514 953 4: 59 802 411 152 830 4: 508 31 37 670 435 4: 962 985 975 117 819 4: 496 322 570 917 832 4: 316 723 616 297 735 4: 39 145 508 895 312 4: 621 457 130 600 666 4: 161 57 28 57 957 4: 112 132 69 339 751 4: 578 811 839 18 811 4: 106 333 509 665 573 4: 997 590 645 997 361 4: 589 457 593 351 247 4: 75 691 633 491 334 4: 842 581 109 108 913 4: 166 96 872 225 542 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 6: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:40:32] : LOG : Building guide tree. 6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:40:32] : LOG : Aligning 6: [2025-07-31 04:40:32] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 7: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:40:32] : LOG : Building guide tree. 7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:40:32] : LOG : Aligning 7: [2025-07-31 04:40:32] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 8: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:40:32] : LOG : Building guide tree. 8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:40:32] : LOG : Aligning 8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 9: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:40:32] : LOG : Building guide tree. 9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:40:32] : LOG : Aligning 9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 10: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:40:32] : LOG : Building guide tree. 10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:40:32] : LOG : Aligning 10: [2025-07-31 04:40:32] : 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:40:32] : LOG : Detected protein sequences. 11: [2025-07-31 04:40:32] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances 11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2025-07-31 04:40:32] : LOG : Building guide tree. 11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: [2025-07-31 04:40:32] : LOG : Aligning 11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2025-07-31 04:40:32] : LOG : DSSim - a simplistic sequence simulator. 12: [2025-07-31 04:40:32] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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[============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2025-07-31 04:41:03] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.55 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 43.01 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-avx 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/reproducible-path/kalign-3.4.0/obj-avx/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2025-07-31 04:41:07] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2025-07-31 04:41:07] : 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: [2025-07-31 04:41:13] : LOG : Timing DYN 256 1: [2025-07-31 04:41:14] : LOG : 1.505487 - dyn 1: [2025-07-31 04:41:14] : LOG : 0.000000 - bpm 1: [2025-07-31 04:41:14] : LOG : 0.090714 - bpm_block2 1: [2025-07-31 04:41:14] : LOG : 0.085631 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.12 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 3: Test timeout computed to be: 1500 3: [2025-07-31 04:41:14] : LOG : Check for correctness. 3: [2025-07-31 04:41:14] : LOG : Timing serial 3: [2025-07-31 04:41:14] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 4: Test timeout computed to be: 1500 4: 224 915 55 565 134 4: 656 53 656 283 410 4: 15 54 351 308 141 4: 928 798 604 436 591 4: 460 666 227 993 713 4: 466 712 670 612 711 4: 152 143 728 666 654 4: 108 926 37 657 969 4: 691 116 286 492 564 4: 773 928 367 646 606 4: 899 601 660 821 542 4: 811 717 528 907 267 4: 757 136 849 38 761 4: 655 759 65 55 173 4: 897 644 560 233 592 4: 935 91 353 123 981 4: 501 55 299 437 256 4: 616 109 808 260 742 4: 920 532 900 704 153 4: 696 637 984 755 745 4: 586 229 471 71 551 4: 780 803 195 539 502 4: 88 32 99 976 309 4: 673 886 334 530 973 4: 88 827 304 164 858 4: 808 280 878 387 746 4: 813 304 0 211 271 4: 235 313 714 842 288 4: 913 938 304 226 936 4: 580 377 893 704 888 4: 271 231 14 85 120 4: 816 572 531 496 983 4: 667 489 388 936 401 4: 90 881 572 696 719 4: 866 348 585 519 926 4: 685 437 463 120 146 4: 5 521 637 57 447 4: 313 617 691 467 236 4: 15 563 798 476 565 4: 588 216 449 166 164 4: 667 147 771 941 912 4: 342 957 767 170 172 4: 144 846 984 36 901 4: 287 508 312 509 69 4: 805 556 848 508 965 4: 424 4 797 76 919 4: 158 336 141 218 624 4: 645 632 387 191 713 4: 239 591 791 511 805 4: 969 613 158 513 998 4: 190 347 205 454 9 4: 363 33 11 116 990 4: 399 695 265 838 29 4: 420 945 314 655 38 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 6: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:14] : LOG : Building guide tree. 6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:14] : LOG : Aligning 6: [2025-07-31 04:41:14] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 7: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:14] : LOG : Building guide tree. 7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:14] : LOG : Aligning 7: [2025-07-31 04:41:14] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 8: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:14] : LOG : Building guide tree. 8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:14] : LOG : Aligning 8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 9: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:14] : LOG : Building guide tree. 9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:14] : LOG : Aligning 9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 10: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:14] : LOG : Building guide tree. 10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:14] : LOG : Aligning 10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:14] : LOG : Detected protein sequences. 11: [2025-07-31 04:41:14] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances 11: [2025-07-31 04:41:14] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 11: [2025-07-31 04:41:14] : LOG : Building guide tree. 11: [2025-07-31 04:41:15] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:01.00 11: [2025-07-31 04:41:15] : LOG : Aligning 11: [2025-07-31 04:41:15] : LOG : CPU Time: 0.03u 00:00:00.03 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2025-07-31 04:41:15] : LOG : DSSim - a simplistic sequence simulator. 12: [2025-07-31 04:41:15] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== 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[============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2025-07-31 04:41:47] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.97 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 43.18 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Test project /build/reproducible-path/kalign-3.4.0/obj-sse4.1 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/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/bpm_utest 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 1: [2025-07-31 04:41:51] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: [2025-07-31 04:41:51] : 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: [2025-07-31 04:41:56] : LOG : Timing DYN 256 1: [2025-07-31 04:41:58] : LOG : 1.512151 - dyn 1: [2025-07-31 04:41:58] : LOG : 0.000000 - bpm 1: [2025-07-31 04:41:58] : LOG : 0.088926 - bpm_block2 1: [2025-07-31 04:41:58] : LOG : 0.085212 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 7.16 sec test 2 Start 2: alphabet_utest 2: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/alphabet_utest 2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 2: Test timeout computed to be: 1500 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 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 3: Test timeout computed to be: 1500 3: [2025-07-31 04:41:58] : LOG : Check for correctness. 3: [2025-07-31 04:41:58] : LOG : Timing serial 3: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 4: Test timeout computed to be: 1500 4: 385 790 951 245 399 4: 179 366 677 472 878 4: 861 401 315 703 921 4: 144 906 956 699 477 4: 889 872 464 467 392 4: 47 969 72 306 322 4: 316 835 941 178 770 4: 104 40 752 668 529 4: 845 9 904 287 834 4: 939 2 158 442 377 4: 964 488 22 887 227 4: 389 453 962 113 739 4: 832 228 204 309 595 4: 970 317 686 307 892 4: 436 913 89 612 24 4: 571 357 691 951 415 4: 688 982 948 358 979 4: 278 731 596 754 686 4: 331 876 994 776 46 4: 431 491 840 316 73 4: 543 290 986 379 132 4: 975 652 829 245 461 4: 499 994 986 284 58 4: 481 636 270 2 358 4: 773 264 301 706 682 4: 256 18 135 581 481 4: 191 468 756 1 174 4: 720 194 933 833 715 4: 506 284 355 151 836 4: 908 70 108 527 378 4: 446 940 358 665 314 4: 341 760 577 212 233 4: 925 20 213 744 605 4: 980 932 409 641 7 4: 691 232 348 729 461 4: 483 928 276 15 577 4: 481 545 220 74 799 4: 841 639 456 984 562 4: 380 79 914 787 770 4: 457 137 45 462 791 4: 572 299 444 223 242 4: 566 746 703 634 208 4: 354 622 942 692 690 4: 640 482 932 47 657 4: 161 632 554 651 287 4: 551 724 151 298 591 4: 276 133 377 148 586 4: 405 457 583 752 209 4: 772 427 290 845 717 4: 69 709 524 697 884 4: 3 443 369 901 667 4: 911 137 830 311 123 4: 795 862 815 814 79 4: 816 0 3 352 725 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib 5: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/kaligncpp 5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 5: Test timeout computed to be: 1500 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 5/12 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa 6: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" 6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 6: Test timeout computed to be: 1500 6: 6: Kalign (3.4.0) 6: 6: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 6: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. 6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:58] : LOG : Building guide tree. 6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: [2025-07-31 04:41:58] : LOG : Aligning 6: [2025-07-31 04:41:58] : 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 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf 7: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 7: Test timeout computed to be: 1500 7: 7: Kalign (3.4.0) 7: 7: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 7: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. 7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:58] : LOG : Building guide tree. 7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: [2025-07-31 04:41:58] : LOG : Aligning 7: [2025-07-31 04:41:58] : 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 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec test 8 Start 8: kalign_itest_BB12006.msf 8: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" 8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 8: Test timeout computed to be: 1500 8: 8: Kalign (3.4.0) 8: 8: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 8: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. 8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:58] : LOG : Building guide tree. 8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: [2025-07-31 04:41:58] : LOG : Aligning 8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 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---- 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa 9: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 9: Test timeout computed to be: 1500 9: 9: Kalign (3.4.0) 9: 9: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 9: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:58] : LOG : Building guide tree. 9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: [2025-07-31 04:41:58] : LOG : Aligning 9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.00 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---- 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 10: 10: Kalign (3.4.0) 10: 10: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 10: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. 10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:58] : LOG : Building guide tree. 10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: [2025-07-31 04:41:58] : LOG : Aligning 10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 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---- 10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa 11: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" 11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 11: Test timeout computed to be: 1500 11: 11: Kalign (3.4.0) 11: 11: Copyright (C) 2006,2019,2020,2021,2023 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: [2025-07-31 04:41:58] : LOG : Detected protein sequences. 11: [2025-07-31 04:41:58] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. 11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 11: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances 11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 11: [2025-07-31 04:41:58] : LOG : Building guide tree. 11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: [2025-07-31 04:41:58] : LOG : Aligning 11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.03u 00:00:00.02 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 11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec test 12 Start 12: DSSIM_takes_a_min 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 12: [2025-07-31 04:41:58] : LOG : DSSim - a simplistic sequence simulator. 12: [2025-07-31 04:41:58] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% 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[============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% 12: [2025-07-31 04:42:30] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% 12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.94 sec 100% tests passed, 0 tests failed out of 12 Total Test time (real) = 43.21 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/libkalign.a -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/include/kalign/kalign_export.h -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignTargets-none.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfig.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/lib/x86_64-linux-gnu/cmake/kalign/kalignConfigVersion.cmake -- Installing: /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin/kalign make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' rm -rf debian/kalign/usr/lib/x86_64-linux-gnu/ dh_install obj-x86_64-linux-gnu/src/kalignfmt usr/bin mkdir -p debian/kalign/usr/lib/kalign/bin cp obj-avx2/src/kalign debian/kalign/usr/lib/kalign/kalign-avx2 cp obj-avx/src/kalign debian/kalign/usr/lib/kalign/kalign-avx cp obj-sse4.1/src/kalign debian/kalign/usr/lib/kalign/kalign-sse4.1 cp obj-avx2/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx2 cp obj-avx/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-avx cp obj-sse4.1/src/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-sse4.1 mv debian/kalign/usr/bin/kalign debian/kalign/usr/lib/kalign/kalign-plain mv debian/kalign/usr/bin/kalignfmt debian/kalign/usr/lib/kalign/kalignfmt-plain dh_install -pkalign debian/bin/simd-dispatch /usr/lib/kalign/bin cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalign cd /build/reproducible-path/kalign-3.4.0/debian/kalign/usr/bin && \ ln -s ../lib/kalign/bin/simd-dispatch kalignfmt make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' 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 debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_md5sums dh_builddeb dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.4.0-1_amd64.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.4.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.4.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../kalign_3.4.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2208375 and its subdirectories I: Current time: Thu Jul 31 18:42:50 +14 2025 I: pbuilder-time-stamp: 1753936970 + false + set +x Thu Jul 31 04:42:50 UTC 2025 I: Signing ./b2/kalign_3.4.0-1_amd64.buildinfo as kalign_3.4.0-1_amd64.buildinfo.asc Thu Jul 31 04:42:50 UTC 2025 I: Signed ./b2/kalign_3.4.0-1_amd64.buildinfo as ./b2/kalign_3.4.0-1_amd64.buildinfo.asc Thu Jul 31 04:42:50 UTC 2025 - build #2 for kalign/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Jul 31 04:42:50 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-IMw798F0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ: total 972 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 04:38 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 04:42 b2 -rw-r--r-- 1 jenkins jenkins 1962 Apr 2 2024 kalign_3.4.0-1.dsc -rw------- 1 jenkins jenkins 975506 Jul 31 04:38 rbuildlog.xYleqpp /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1: total 2692 -rw-r--r-- 1 jenkins jenkins 972166 Jul 31 04:38 build.log -rw-r--r-- 1 jenkins jenkins 674184 Jul 31 04:38 kalign-dbgsym_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12372 Jul 31 04:38 kalign_3.4.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1962 Jul 31 04:38 kalign_3.4.0-1.dsc -rw-r--r-- 1 jenkins jenkins 5888 Jul 31 04:38 kalign_3.4.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6770 Jul 31 04:38 kalign_3.4.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1380 Jul 31 04:38 kalign_3.4.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 137544 Jul 31 04:38 kalign_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1495 Jul 31 04:38 kalign_3.4.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 903277 Jul 31 04:38 kalign_3.4.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2: total 2676 -rw-r--r-- 1 jenkins jenkins 974078 Jul 31 04:42 build.log -rw-r--r-- 1 jenkins jenkins 674184 Jul 31 04:42 kalign-dbgsym_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12372 Jul 31 04:42 kalign_3.4.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1962 Jul 31 04:42 kalign_3.4.0-1.dsc -rw-r--r-- 1 jenkins jenkins 5875 Jul 31 04:42 kalign_3.4.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6757 Jul 31 04:42 kalign_3.4.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1380 Jul 31 04:42 kalign_3.4.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 137544 Jul 31 04:42 kalign_3.4.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1495 Jul 31 04:42 kalign_3.4.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 903277 Jul 31 04:42 kalign_3.4.0.orig.tar.gz Thu Jul 31 04:42:51 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Jul 31 04:42:51 UTC 2025 I: kalign_3.4.0-1_amd64.changes: Format: 1.8 Date: Tue, 02 Apr 2024 13:49:50 +0200 Source: kalign Binary: kalign kalign-dbgsym Architecture: amd64 Version: 1:3.4.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: kalign - Global and progressive multiple sequence alignment Changes: kalign (1:3.4.0-1) unstable; urgency=medium . * Team upload. * New upstream version * d/patches: disable pass-proper-flags.patch for now. Checksums-Sha1: 0a8baa4a2aa4424dd60f2f091f1bf327bfc07bc3 674184 kalign-dbgsym_3.4.0-1_amd64.deb 48964d89e4144eb1149284874e5926a154091142 5888 kalign_3.4.0-1_amd64.buildinfo 89939e22790ce62c610b6645f51e76b19287d224 137544 kalign_3.4.0-1_amd64.deb Checksums-Sha256: 359430a5ae522631901503e2c05f1d87bc94392d2e2d472bb23044136c031309 674184 kalign-dbgsym_3.4.0-1_amd64.deb 88cedee597ea8e28f9d5b8c0cfd505b40520415fe9eed36127c7e3a1c41d7146 5888 kalign_3.4.0-1_amd64.buildinfo e3449f0886600889fd6773603cb41d2e039bb24bb6b27a7cc8b285ba1d23a31b 137544 kalign_3.4.0-1_amd64.deb Files: b8033b36e8d3f3989c7cf3e06a5f6c05 674184 debug optional kalign-dbgsym_3.4.0-1_amd64.deb 13f6aa6d5f789b428072a77aabd6705d 5888 science optional kalign_3.4.0-1_amd64.buildinfo 1d8e18ceb8472fc301d4ef63fd0389fa 137544 science optional kalign_3.4.0-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/kalign_3.4.0-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/kalign_3.4.0-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/kalign_3.4.0-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/kalign_3.4.0-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/kalign_3.4.0-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/kalign_3.4.0-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-07-31 04:38:52.452348319 +0000 +++ b2/build.log 2025-07-31 04:42:51.432659986 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 1 22:55:51 -12 2026 -I: pbuilder-time-stamp: 1788346551 +I: Current time: Thu Jul 31 18:38:54 +14 2025 +I: pbuilder-time-stamp: 1753936734 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 31 04:39 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8fee02fc933e4602b39349a6300fdb23' - 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='1867936' - PS1='# ' - PS2='> ' + INVOCATION_ID=511f0f45f685463fa5b8ae9d39cb16b6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2208375 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.u98MuRLQ/pbuilderrc_uT3F --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/pbuilderrc_ZF1P --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2 --logfile b2/build.log kalign_3.4.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1867936/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -167,7 +199,7 @@ Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 31.9 MB in 6s (5250 kB/s) +Fetched 31.9 MB in 3s (9365 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19850 files and directories currently installed.) @@ -422,7 +454,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kalign-3.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kalign_3.4.0-1_source.changes +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kalign-3.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kalign_3.4.0-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.4.0-1 dpkg-buildpackage: info: source distribution unstable @@ -473,8 +509,8 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (4.7s) --- Generating done (0.2s) +-- Configuring done (1.4s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -523,8 +559,8 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (9.3s) --- Generating done (0.2s) +-- Configuring done (1.6s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -576,7 +612,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (11.6s) +-- Configuring done (2.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -632,8 +668,8 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (7.9s) --- Generating done (0.2s) +-- Configuring done (4.2s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -646,7 +682,7 @@ -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx2 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -657,11 +693,11 @@ make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' @@ -672,90 +708,102 @@ cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build +make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -[ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -[ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -[ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -[ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -[ 9%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -[ 10%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +[ 12%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +[ 12%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o +[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +[ 12%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 16%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 16%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +[ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +[ 18%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +[ 22%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +[ 28%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +[ 33%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +[ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -[ 14%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -[ 14%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +[ 13%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o +[ 41%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +[ 41%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +[ 41%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -[ 16%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 17%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -[ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -[ 21%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c -[ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -[ 24%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 27%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -[ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -[ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -[ 33%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o 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lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. 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-I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; @@ -774,49 +822,38 @@ /build/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF 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-DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c -[ 66%] Linking C executable task_utest -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c +[ 66%] Linking C executable alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 67%] Linking C executable bpm_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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+[ 68%] Linking C static library libtldevel.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 68%] Built target alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 68%] Linking C executable alphabet_utest -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +[ 70%] Linking C executable task_utest +/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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 68%] Built target task_utest -[ 68%] Built target bpm_utest -[ 70%] Linking C executable edist_utest -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 [ 70%] 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 @@ -824,138 +861,108 @@ cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 70%] Built target tldevel make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 71%] Linking C static library libkalign.a -[ 72%] Linking C static library libkalign_static.a -[ 72%] Built target alphabet_utest -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake +make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 70%] Built target bpm_utest +[ 71%] Linking C static library libkalign_static.a +[ 72%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake -[ 72%] Built target edist_utest -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake +[ 74%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 -[ 74%] Linking C static library libtldevel.a -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +[ 74%] Built target task_utest +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/ar qc libkalign.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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a /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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign_static.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 74%] Built target edist_utest [ 74%] Built target kalign -[ 74%] Built target kalign_static +make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend +make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend +[ 74%] Built target kalign_static make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu 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'/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/build -make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f 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tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -MF CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o.d -o CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_cmp_test.c -make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend -make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend -make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c -[ 91%] Linking C executable kalign_cmp_test -[ 90%] Linking C executable kalign_io_test -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 -[ 93%] Linking C executable kalign_lib_test -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", @@ -969,24 +976,53 @@ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | 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largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[100%] Built target dssim +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 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lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection 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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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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 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lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. 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lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 22%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -[ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -[ 29%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 27%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_io.c +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c -[ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c +/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': +/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] + 58 | float d2; + | ^~ +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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); @@ -1119,10 +1155,6 @@ /build/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': -/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] - 58 | float d2; - | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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); @@ -1130,20 +1162,26 @@ /build/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o [ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c -[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 64%] Built target kalign_OBJ +[ 66%] Linking C executable alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +[ 66%] 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/reproducible-path/kalign-3.4.0/obj-sse4.1' @@ -1151,145 +1189,136 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build +make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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-DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +[ 91%] Built target kalign_cmp_test +[ 91%] Built target kalign_io_test +[ 93%] Linking C executable kalign_lib_test +[ 94%] Linking C executable kalignfmt +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", @@ -1303,28 +1332,35 @@ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 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+[ 94%] Built target kalign_lib_test +[ 98%] Linking C executable dssim +[ 98%] Linking C executable largebench +[ 98%] Linking C executable kalign +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 +[100%] Linking CXX executable kaligncpp +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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-Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[100%] Linking CXX executable kaligncpp -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 -[100%] Built target dssim -[100%] Built target largebench /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +[100%] Built target kalign-bin +[100%] Built target dssim [100%] Built target kaligncpp make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-sse4.1/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' dh_auto_build --builddirectory obj-avx - cd obj-avx && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-avx && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-avx//CMakeFiles/progress.marks @@ -1337,9 +1373,9 @@ make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib /build/reproducible-path/kalign-3.4.0/obj-avx/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' @@ -1351,13 +1387,13 @@ make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build +make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' @@ -1366,90 +1402,90 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 1%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 5%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -[ 6%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -[ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +[ 2%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +[ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +[ 4%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +[ 5%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o +[ 8%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o +[ 9%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +[ 10%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +[ 10%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 13%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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/build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration 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/usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/task.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c +[ 29%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration 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lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. 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-Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 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/build/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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/build/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': +/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] + 58 | float d2; + | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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); @@ -1457,10 +1493,6 @@ /build/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': -/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] - 58 | float d2; - | ^~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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); @@ -1468,164 +1500,179 @@ /build/reproducible-path/kalign-3.4.0/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c -[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT 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-o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c [ 66%] Linking C executable bpm_utest -[ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +[ 67%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +[ 71%] Built target bpm_utest +[ 71%] Linking C executable task_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 70%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d CMakeFiles/edist_utest.dir/src/tldevel.c.o 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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 -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +[ 71%] Built target tldevel make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build -make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 72%] Linking C static library libkalign_static.a -[ 74%] Linking C static library libkalign.a -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P 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edist_utest [ 74%] Built target task_utest -/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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o 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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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a +/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 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/usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c -[ 90%] Linking C executable kalign_cmp_test -[ 91%] Linking C executable kalign_io_test -cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 +[ 90%] Linking C executable kalign_io_test cd 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CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[100%] Built target dssim make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' dh_auto_build --builddirectory obj-avx2 - cd obj-avx2 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-avx2 && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-avx2//CMakeFiles/progress.marks @@ -1673,11 +1709,11 @@ make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend -make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' @@ -1689,105 +1725,101 @@ make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build -make[4]: 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Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration 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CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration 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lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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&& /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 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CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_op.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -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/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 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lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_check.c +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/task.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/bpm.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c +[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c +cd 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_param.c -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/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); @@ -1802,34 +1834,32 @@ /build/reproducible-path/kalign-3.4.0/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_seqprofile.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_run.c +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. 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/build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c -[ 67%] Linking C executable task_utest -[ 67%] Linking C static library libtldevel.a -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d CMakeFiles/task_utest.dir/src/tldevel.c.o 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lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -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/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP 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+cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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/reproducible-path/kalign-3.4.0/obj-avx2' -[ 67%] Built target task_utest -/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 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 68%] Linking C executable edist_utest -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 -[ 68%] Built target kalign_OBJ -[ 68%] Built target tldevel +[ 67%] 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/reproducible-path/kalign-3.4.0/obj-avx2' @@ -1837,114 +1867,129 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/kalign_static.dir/build.make 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-fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d 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 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 +[ 70%] Linking C static library libkalign.a +[ 70%] Linking C static library libkalign_static.a +[ 70%] Built target alphabet_utest +[ 70%] Built target edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 -[ 74%] Built target edist_utest +[ 74%] Linking C executable task_utest +[ 72%] Linking C static library libtldevel.a +[ 74%] Linking C executable bpm_utest +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d 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 +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 74%] Built target task_utest [ 74%] Built target bpm_utest -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +/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/reproducible-path/kalign-3.4.0/obj-avx2' -[ 74%] Built target alphabet_utest /usr/bin/ar qc libkalign.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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a +/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/msa_sort.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 CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o 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to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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kaligncpp -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +[ 98%] Linking C executable dssim +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 +[100%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[100%] Linking C executable dssim -[100%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[100%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +[100%] Built target largebench make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[100%] Built target kalign-bin +[100%] Built target dssim /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' [100%] Built target kaligncpp -[100%] Built target largebench -[100%] Built target dssim -[100%] Built target kalign-bin make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -2086,7 +2122,7 @@ 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-09-02 10:58:50] : LOG : Testing correctness of serial bpm. +1: [2025-07-31 04:39:47] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -2219,63 +2255,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2026-09-02 10:58:50] : LOG : Check for correctness. -3: [2026-09-02 10:58:50] : LOG : Timing serial -3: [2026-09-02 10:58:50] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -4: 788 155 210 635 401 -4: 507 120 774 344 924 -4: 889 420 796 445 812 -4: 349 560 367 696 303 -4: 740 752 448 307 684 -4: 809 976 104 100 175 -4: 671 356 827 39 217 -4: 2 911 832 268 77 -4: 385 24 925 582 905 -4: 746 562 431 232 797 -4: 237 97 712 948 156 -4: 72 438 373 175 146 -4: 954 318 468 315 221 -4: 307 596 927 27 557 -4: 410 518 446 166 536 -4: 462 637 808 494 542 -4: 550 337 980 820 288 -4: 662 140 596 231 173 -4: 256 291 169 514 793 -4: 653 899 664 830 662 -4: 808 259 453 369 749 -4: 142 313 880 348 356 -4: 150 429 82 812 359 -4: 817 275 275 616 824 -4: 340 777 787 896 831 -4: 982 999 204 627 934 -4: 945 83 118 284 508 -4: 902 448 661 193 62 -4: 842 291 732 543 433 -4: 55 721 302 143 80 -4: 698 573 487 688 884 -4: 248 190 441 919 405 -4: 142 129 937 999 819 -4: 296 495 126 175 117 -4: 8 500 318 826 54 -4: 11 932 74 499 283 -4: 53 340 88 27 386 -4: 372 183 756 850 63 -4: 480 431 175 918 106 -4: 71 386 955 333 577 -4: 909 886 343 277 964 -4: 151 686 41 779 849 -4: 144 877 889 950 157 -4: 843 71 311 299 225 -4: 821 795 153 327 97 -4: 735 808 780 916 462 -4: 385 519 483 131 884 -4: 939 938 33 984 553 -4: 1 412 823 846 159 -4: 938 2 247 797 231 -4: 49 581 663 670 829 -4: 149 684 369 815 524 -4: 640 804 513 803 432 -4: 618 348 493 82 122 +3: [2025-07-31 04:39:47] : LOG : Check for correctness. +3: [2025-07-31 04:39:47] : LOG : Timing serial +3: [2025-07-31 04:39:47] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +4: 176 596 917 495 951 +4: 889 193 524 787 661 +4: 691 561 765 759 771 +4: 227 623 645 750 227 +4: 714 679 372 198 377 +4: 973 651 59 655 15 +4: 64 224 236 305 396 +4: 952 450 6 843 587 +4: 122 147 580 234 558 +4: 346 419 672 553 649 +4: 678 753 661 51 279 +4: 616 946 108 439 435 +4: 622 881 219 965 450 +4: 955 872 208 51 69 +4: 15 81 296 184 311 +4: 381 702 189 139 128 +4: 703 61 745 472 195 +4: 980 134 119 684 305 +4: 350 212 497 613 729 +4: 257 855 608 390 839 +4: 990 854 160 798 579 +4: 948 738 922 542 25 +4: 289 107 38 558 275 +4: 698 366 107 413 333 +4: 235 237 21 691 313 +4: 1 798 917 296 30 +4: 304 124 759 758 852 +4: 463 994 444 990 177 +4: 919 719 988 280 50 +4: 202 238 469 782 948 +4: 207 462 919 195 882 +4: 950 877 519 736 134 +4: 911 757 247 123 287 +4: 617 285 231 444 748 +4: 531 547 690 800 590 +4: 714 224 496 235 397 +4: 818 548 877 52 460 +4: 269 943 592 461 597 +4: 548 616 302 621 388 +4: 254 676 353 107 648 +4: 408 675 588 832 7 +4: 355 133 123 486 754 +4: 934 410 166 654 139 +4: 562 37 555 636 429 +4: 582 483 383 822 634 +4: 44 161 697 306 228 +4: 590 97 620 696 645 +4: 222 622 120 126 386 +4: 553 750 419 805 585 +4: 5 625 556 748 227 +4: 147 644 348 43 903 +4: 305 68 330 7 249 +4: 463 185 707 640 869 +4: 806 491 371 350 404 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK @@ -2297,15 +2333,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -6: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:58:50] : LOG : Building guide tree. -6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:58:50] : LOG : Aligning -6: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +6: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:39:47] : LOG : Building guide tree. +6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:39:47] : LOG : Aligning +6: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2334,15 +2370,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -7: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:58:50] : LOG : Building guide tree. -7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:58:50] : LOG : Aligning -7: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +7: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:39:47] : LOG : Building guide tree. +7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:39:47] : LOG : Aligning +7: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2371,15 +2407,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -8: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:58:50] : LOG : Building guide tree. -8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:58:50] : LOG : Aligning -8: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +8: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:39:47] : LOG : Building guide tree. +8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:39:47] : LOG : Aligning +8: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2420,15 +2456,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -9: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:58:50] : LOG : Building guide tree. -9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:58:50] : LOG : Aligning -9: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +9: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:39:47] : LOG : Building guide tree. +9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:39:47] : LOG : Aligning +9: [2025-07-31 04:39:47] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2469,15 +2505,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -10: [2026-09-02 10:58:50] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:58:50] : LOG : Building guide tree. -10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:58:50] : LOG : Aligning -10: [2026-09-02 10:58:50] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +10: [2025-07-31 04:39:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:39:47] : LOG : Building guide tree. +10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:39:47] : LOG : Aligning +10: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2503,8 +2539,8 @@ 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- 1/12 Test #2: alphabet_utest ................... Passed 0.02 sec - 2/12 Test #3: edist_utest ...................... Passed 0.02 sec - 3/12 Test #4: task_utest ....................... Passed 0.02 sec + 2/12 Test #3: edist_utest ...................... Passed 0.01 sec + 3/12 Test #4: task_utest ....................... Passed 0.01 sec 4/12 Test #5: C++Lib ........................... Passed 0.01 sec 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec @@ -2527,17 +2563,17 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2026-09-02 10:58:50] : LOG : Detected protein sequences. -11: [2026-09-02 10:58:50] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-09-02 10:58:50] : LOG : Calculating pairwise distances -12: [2026-09-02 10:58:50] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-09-02 10:58:50] : LOG : Protein alignments - 20 seq -11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2026-09-02 10:58:50] : LOG : Building guide tree. -11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -11: [2026-09-02 10:58:50] : LOG : Aligning -11: [2026-09-02 10:58:50] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2025-07-31 04:39:47] : LOG : Detected protein sequences. +11: [2025-07-31 04:39:47] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-07-31 04:39:47] : LOG : Calculating pairwise distances +12: [2025-07-31 04:39:47] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-07-31 04:39:47] : LOG : Protein alignments - 20 seq +11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +11: [2025-07-31 04:39:47] : LOG : Building guide tree. +11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2025-07-31 04:39:47] : LOG : Aligning +11: [2025-07-31 04:39:47] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -2852,35 +2888,35 @@ 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2026-09-02 10:58:50] : LOG : 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-09-02 10:58:53] : LOG : Protein alignments - 1000 seq +12: [2025-07-31 04:39:51] : LOG : Protein alignments - 1000 seq 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: [2026-09-02 10:58:55] : LOG : Timing DYN 256 -1: [2026-09-02 10:58:57] : LOG : 1.557818 - dyn -1: [2026-09-02 10:58:57] : LOG : 0.000000 - bpm -1: [2026-09-02 10:58:57] : LOG : 0.089773 - bpm_block2 -1: [2026-09-02 10:58:57] : LOG : 0.085551 - bpm_block -11/12 Test #1: bpm_utest ........................ Passed 7.19 sec +1: [2025-07-31 04:39:53] : LOG : Timing DYN 256 +1: [2025-07-31 04:39:54] : LOG : 1.480885 - dyn +1: [2025-07-31 04:39:54] : LOG : 0.000000 - bpm +1: [2025-07-31 04:39:54] : LOG : 0.090882 - bpm_block2 +1: [2025-07-31 04:39:54] : LOG : 0.085667 - bpm_block +11/12 Test #1: bpm_utest ........................ Passed 7.13 sec 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 10:59:05] : LOG : Protein alignments - 10000 seq +12: [2025-07-31 04:40:01] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2026-09-02 10:59:14] : LOG : DNA alignments - 20 seq +12: [2025-07-31 04:40:11] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 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[==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-09-02 10:59:17] : LOG : DNA alignments - 1000 seq +12: [2025-07-31 04:40:14] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 10:59:23] : LOG : DNA alignments - 10000 seq +12: [2025-07-31 04:40:20] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 37.03 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.06 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 37.28 sec +Total Test time (real) = 36.08 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' @@ -2909,25 +2945,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-09-02 10:59:28] : LOG : Testing correctness of serial bpm. +1: [2025-07-31 04:40:24] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2026-09-02 10:59:28] : LOG : Testing correctness of AVX bpm. +1: [2025-07-31 04:40:24] : 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: [2026-09-02 10:59:34] : LOG : Timing DYN 256 -1: [2026-09-02 10:59:36] : LOG : 1.557887 - dyn -1: [2026-09-02 10:59:36] : LOG : 0.056407 - bpm -1: [2026-09-02 10:59:36] : LOG : 0.090412 - bpm_block2 -1: [2026-09-02 10:59:36] : LOG : 0.086362 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 7.59 sec +1: [2025-07-31 04:40:30] : LOG : Timing DYN 256 +1: [2025-07-31 04:40:32] : LOG : 1.512778 - dyn +1: [2025-07-31 04:40:32] : LOG : 0.058957 - bpm +1: [2025-07-31 04:40:32] : LOG : 0.090890 - bpm_block2 +1: [2025-07-31 04:40:32] : LOG : 0.084968 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 7.36 sec test 2 Start 2: alphabet_utest @@ -3073,11 +3109,11 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 3: Test timeout computed to be: 1500 -3: [2026-09-02 10:59:36] : LOG : Check for correctness. -3: [2026-09-02 10:59:36] : LOG : Timing serial -3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -3: [2026-09-02 10:59:36] : LOG : Timing AVX -3: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2025-07-31 04:40:32] : LOG : Check for correctness. +3: [2025-07-31 04:40:32] : LOG : Timing serial +3: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2025-07-31 04:40:32] : LOG : Timing AVX +3: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -3085,60 +3121,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 4: Test timeout computed to be: 1500 -4: 696 126 292 831 552 -4: 324 318 197 51 270 -4: 509 210 42 368 248 -4: 516 251 616 292 569 -4: 437 824 628 256 850 -4: 179 275 732 404 775 -4: 807 872 693 869 605 -4: 808 558 806 292 991 -4: 724 628 609 414 993 -4: 299 375 781 741 67 -4: 888 149 875 370 10 -4: 824 899 623 867 31 -4: 886 477 872 40 341 -4: 261 137 370 45 893 -4: 551 37 190 734 70 -4: 458 928 221 190 573 -4: 670 274 165 936 452 -4: 188 868 292 41 325 -4: 997 786 314 427 262 -4: 947 398 892 590 507 -4: 421 386 79 344 22 -4: 838 290 253 359 956 -4: 525 565 966 278 56 -4: 147 376 273 137 117 -4: 24 971 394 918 330 -4: 721 845 744 578 679 -4: 755 557 536 791 62 -4: 83 327 545 631 824 -4: 379 165 822 389 588 -4: 620 326 649 691 292 -4: 140 798 498 483 889 -4: 927 913 152 320 427 -4: 120 460 244 449 454 -4: 592 279 795 561 304 -4: 21 271 450 381 577 -4: 651 264 302 843 419 -4: 868 941 69 508 210 -4: 213 776 176 810 851 -4: 582 484 807 368 771 -4: 539 839 686 140 819 -4: 750 657 242 66 510 -4: 353 399 31 344 359 -4: 442 234 950 166 626 -4: 111 261 236 908 216 -4: 340 15 546 902 316 -4: 654 19 378 380 879 -4: 305 807 344 916 904 -4: 492 864 81 330 18 -4: 963 771 305 547 889 -4: 422 627 614 300 389 -4: 30 279 691 328 568 -4: 248 942 286 120 666 -4: 807 907 837 979 149 -4: 251 791 532 875 505 +4: 854 498 246 170 313 +4: 619 617 81 150 721 +4: 322 616 867 187 651 +4: 238 622 83 186 29 +4: 602 202 883 957 346 +4: 124 884 557 497 137 +4: 504 414 926 632 651 +4: 423 382 251 145 300 +4: 527 341 740 75 286 +4: 530 451 241 166 557 +4: 585 767 756 422 550 +4: 508 528 913 455 27 +4: 912 971 262 294 329 +4: 50 387 988 176 855 +4: 133 571 295 702 859 +4: 950 767 98 393 789 +4: 582 482 355 25 460 +4: 753 356 885 276 605 +4: 44 78 452 979 995 +4: 631 446 886 446 366 +4: 681 844 865 143 474 +4: 4 758 560 817 405 +4: 665 981 405 132 163 +4: 353 718 848 965 318 +4: 357 333 956 189 542 +4: 334 687 809 800 493 +4: 233 387 720 453 610 +4: 800 867 181 766 276 +4: 283 227 413 965 178 +4: 520 350 251 521 603 +4: 194 20 458 382 184 +4: 617 46 901 946 488 +4: 483 722 120 55 291 +4: 494 956 970 102 904 +4: 437 340 75 386 789 +4: 72 810 854 511 507 +4: 666 349 801 882 806 +4: 415 353 771 514 953 +4: 59 802 411 152 830 +4: 508 31 37 670 435 +4: 962 985 975 117 819 +4: 496 322 570 917 832 +4: 316 723 616 297 735 +4: 39 145 508 895 312 +4: 621 457 130 600 666 +4: 161 57 28 57 957 +4: 112 132 69 339 751 +4: 578 811 839 18 811 +4: 106 333 509 665 573 +4: 997 590 645 997 361 +4: 589 457 593 351 247 +4: 75 691 633 491 334 +4: 842 581 109 108 913 +4: 166 96 872 225 542 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -3174,15 +3210,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -6: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:59:36] : LOG : Building guide tree. -6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 10:59:36] : LOG : Aligning -6: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +6: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:40:32] : LOG : Building guide tree. +6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:40:32] : LOG : Aligning +6: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3195,7 +3231,7 @@ 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec + 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf @@ -3218,15 +3254,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -7: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:59:36] : LOG : Building guide tree. -7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 10:59:36] : LOG : Aligning -7: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +7: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:40:32] : LOG : Building guide tree. +7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:40:32] : LOG : Aligning +7: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3262,15 +3298,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -8: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:59:36] : LOG : Building guide tree. -8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 10:59:36] : LOG : Aligning -8: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +8: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:40:32] : LOG : Building guide tree. +8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:40:32] : LOG : Aligning +8: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3318,15 +3354,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -9: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:59:36] : LOG : Building guide tree. -9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 10:59:36] : LOG : Aligning -9: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +9: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:40:32] : LOG : Building guide tree. +9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:40:32] : LOG : Aligning +9: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3374,15 +3410,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -10: [2026-09-02 10:59:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:59:36] : LOG : Building guide tree. -10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 10:59:36] : LOG : Aligning -10: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +10: [2025-07-31 04:40:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:40:32] : LOG : Building guide tree. +10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:40:32] : LOG : Aligning +10: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3430,15 +3466,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2026-09-02 10:59:36] : LOG : Detected protein sequences. -11: [2026-09-02 10:59:36] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-09-02 10:59:36] : LOG : Calculating pairwise distances -11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2026-09-02 10:59:36] : LOG : Building guide tree. -11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2026-09-02 10:59:36] : LOG : Aligning -11: [2026-09-02 10:59:36] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2025-07-31 04:40:32] : LOG : Detected protein sequences. +11: [2025-07-31 04:40:32] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-07-31 04:40:32] : LOG : Calculating pairwise distances +11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +11: [2025-07-31 04:40:32] : LOG : Building guide tree. +11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2025-07-31 04:40:32] : LOG : Aligning +11: [2025-07-31 04:40:32] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -3754,24 +3790,24 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2026-09-02 10:59:36] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-09-02 10:59:36] : LOG : Protein alignments - 20 seq +12: [2025-07-31 04:40:32] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-07-31 04:40:32] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== 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10:59:40] : LOG : Protein alignments - 1000 seq +12: [2025-07-31 04:40:35] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 10:59:51] : LOG : Protein alignments - 10000 seq +12: [2025-07-31 04:40:46] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2026-09-02 11:00:00] : LOG : DNA alignments - 20 seq +12: [2025-07-31 04:40:55] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-09-02 11:00:03] : LOG : DNA alignments - 1000 seq +12: [2025-07-31 04:40:58] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 11:00:09] : LOG : DNA alignments - 10000 seq +12: [2025-07-31 04:41:03] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 37.06 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.55 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 44.76 sec +Total Test time (real) = 43.01 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl @@ -3790,25 +3826,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-09-02 11:00:13] : LOG : Testing correctness of serial bpm. +1: [2025-07-31 04:41:07] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2026-09-02 11:00:13] : LOG : Testing correctness of AVX bpm. +1: [2025-07-31 04:41:07] : 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: [2026-09-02 11:00:19] : LOG : Timing DYN 256 -1: [2026-09-02 11:00:20] : LOG : 1.519412 - dyn -1: [2026-09-02 11:00:20] : LOG : 0.000000 - bpm -1: [2026-09-02 11:00:20] : LOG : 0.090842 - bpm_block2 -1: [2026-09-02 11:00:20] : LOG : 0.085216 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 7.18 sec +1: [2025-07-31 04:41:13] : LOG : Timing DYN 256 +1: [2025-07-31 04:41:14] : LOG : 1.505487 - dyn +1: [2025-07-31 04:41:14] : LOG : 0.000000 - bpm +1: [2025-07-31 04:41:14] : LOG : 0.090714 - bpm_block2 +1: [2025-07-31 04:41:14] : LOG : 0.085631 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 7.12 sec test 2 Start 2: alphabet_utest @@ -3954,9 +3990,9 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 3: Test timeout computed to be: 1500 -3: [2026-09-02 11:00:20] : LOG : Check for correctness. -3: [2026-09-02 11:00:20] : LOG : Timing serial -3: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2025-07-31 04:41:14] : LOG : Check for correctness. +3: [2025-07-31 04:41:14] : LOG : Timing serial +3: [2025-07-31 04:41:14] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -3964,60 +4000,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 4: Test timeout computed to be: 1500 -4: 820 299 907 917 4 -4: 218 483 485 537 832 -4: 316 484 188 840 285 -4: 46 764 740 715 473 -4: 644 903 694 854 191 -4: 972 335 202 485 489 -4: 152 490 474 47 535 -4: 536 139 402 315 738 -4: 148 832 555 372 65 -4: 345 861 463 253 401 -4: 760 625 235 737 140 -4: 739 911 992 192 974 -4: 531 635 522 355 431 -4: 499 614 92 650 677 -4: 177 528 387 122 529 -4: 991 679 1 676 489 -4: 348 674 61 376 731 -4: 596 916 273 859 914 -4: 416 533 436 18 338 -4: 840 555 775 928 820 -4: 611 319 828 23 220 -4: 980 994 47 123 524 -4: 397 668 111 5 491 -4: 424 266 606 271 233 -4: 360 676 973 308 107 -4: 785 730 62 308 188 -4: 681 713 387 797 284 -4: 946 705 250 30 161 -4: 624 567 993 48 794 -4: 519 326 807 720 473 -4: 815 241 67 141 517 -4: 392 70 52 745 664 -4: 431 996 114 736 151 -4: 283 841 765 803 676 -4: 365 674 971 643 348 -4: 405 192 321 126 910 -4: 725 320 510 49 556 -4: 746 531 139 190 188 -4: 260 709 1 926 462 -4: 946 225 435 677 276 -4: 800 564 212 765 181 -4: 487 800 101 499 200 -4: 264 994 914 923 241 -4: 419 156 891 43 128 -4: 3 818 575 240 471 -4: 306 9 629 307 893 -4: 106 343 548 508 739 -4: 129 576 81 636 243 -4: 140 30 954 496 58 -4: 331 55 13 470 888 -4: 588 681 245 234 705 -4: 96 179 327 451 132 -4: 798 458 922 345 968 -4: 130 787 670 989 123 +4: 224 915 55 565 134 +4: 656 53 656 283 410 +4: 15 54 351 308 141 +4: 928 798 604 436 591 +4: 460 666 227 993 713 +4: 466 712 670 612 711 +4: 152 143 728 666 654 +4: 108 926 37 657 969 +4: 691 116 286 492 564 +4: 773 928 367 646 606 +4: 899 601 660 821 542 +4: 811 717 528 907 267 +4: 757 136 849 38 761 +4: 655 759 65 55 173 +4: 897 644 560 233 592 +4: 935 91 353 123 981 +4: 501 55 299 437 256 +4: 616 109 808 260 742 +4: 920 532 900 704 153 +4: 696 637 984 755 745 +4: 586 229 471 71 551 +4: 780 803 195 539 502 +4: 88 32 99 976 309 +4: 673 886 334 530 973 +4: 88 827 304 164 858 +4: 808 280 878 387 746 +4: 813 304 0 211 271 +4: 235 313 714 842 288 +4: 913 938 304 226 936 +4: 580 377 893 704 888 +4: 271 231 14 85 120 +4: 816 572 531 496 983 +4: 667 489 388 936 401 +4: 90 881 572 696 719 +4: 866 348 585 519 926 +4: 685 437 463 120 146 +4: 5 521 637 57 447 +4: 313 617 691 467 236 +4: 15 563 798 476 565 +4: 588 216 449 166 164 +4: 667 147 771 941 912 +4: 342 957 767 170 172 +4: 144 846 984 36 901 +4: 287 508 312 509 69 +4: 805 556 848 508 965 +4: 424 4 797 76 919 +4: 158 336 141 218 624 +4: 645 632 387 191 713 +4: 239 591 791 511 805 +4: 969 613 158 513 998 +4: 190 347 205 454 9 +4: 363 33 11 116 990 +4: 399 695 265 838 29 +4: 420 945 314 655 38 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -4053,15 +4089,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -6: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:00:20] : LOG : Building guide tree. -6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:00:20] : LOG : Aligning -6: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +6: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:14] : LOG : Building guide tree. +6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:14] : LOG : Aligning +6: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4097,15 +4133,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -7: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:00:20] : LOG : Building guide tree. -7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:00:20] : LOG : Aligning -7: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +7: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:14] : LOG : Building guide tree. +7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:14] : LOG : Aligning +7: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4141,15 +4177,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -8: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:00:20] : LOG : Building guide tree. -8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:00:20] : LOG : Aligning -8: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +8: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:14] : LOG : Building guide tree. +8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:14] : LOG : Aligning +8: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4197,15 +4233,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -9: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:00:20] : LOG : Building guide tree. -9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:00:20] : LOG : Aligning -9: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +9: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:14] : LOG : Building guide tree. +9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:14] : LOG : Aligning +9: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4253,15 +4289,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -10: [2026-09-02 11:00:20] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:00:20] : LOG : Building guide tree. -10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:00:20] : LOG : Aligning -10: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +10: [2025-07-31 04:41:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:14] : LOG : Building guide tree. +10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:14] : LOG : Aligning +10: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4309,15 +4345,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2026-09-02 11:00:20] : LOG : Detected protein sequences. -11: [2026-09-02 11:00:20] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-09-02 11:00:20] : LOG : Calculating pairwise distances -11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2026-09-02 11:00:20] : LOG : Building guide tree. -11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2026-09-02 11:00:20] : LOG : Aligning -11: [2026-09-02 11:00:20] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:14] : LOG : Detected protein sequences. +11: [2025-07-31 04:41:14] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-07-31 04:41:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:14] : LOG : Calculating pairwise distances +11: [2025-07-31 04:41:14] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:14] : LOG : Building guide tree. +11: [2025-07-31 04:41:15] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:01.00 +11: [2025-07-31 04:41:15] : LOG : Aligning +11: [2025-07-31 04:41:15] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -4633,24 +4669,24 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2026-09-02 11:00:20] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-09-02 11:00:20] : LOG : Protein alignments - 20 seq +12: [2025-07-31 04:41:15] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-07-31 04:41:15] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 10% 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-09-02 11:00:24] : LOG : Protein alignments - 1000 seq +12: [2025-07-31 04:41:18] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 11:00:36] : LOG : Protein alignments - 10000 seq +12: [2025-07-31 04:41:29] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2026-09-02 11:00:45] : LOG : DNA alignments - 20 seq +12: [2025-07-31 04:41:38] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% 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] 90% [==================================================] 100% -12: [2026-09-02 11:00:54] : LOG : DNA alignments - 10000 seq +12: [2025-07-31 04:41:47] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 38.00 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.97 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 45.28 sec +Total Test time (real) = 43.18 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl @@ -4669,25 +4705,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-09-02 11:00:58] : LOG : Testing correctness of serial bpm. +1: [2025-07-31 04:41:51] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2026-09-02 11:00:59] : LOG : Testing correctness of AVX bpm. +1: [2025-07-31 04:41:51] : 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: [2026-09-02 11:01:04] : LOG : Timing DYN 256 -1: [2026-09-02 11:01:06] : LOG : 1.509283 - dyn -1: [2026-09-02 11:01:06] : LOG : 0.000000 - bpm -1: [2026-09-02 11:01:06] : LOG : 0.089574 - bpm_block2 -1: [2026-09-02 11:01:06] : LOG : 0.087026 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 7.20 sec +1: [2025-07-31 04:41:56] : LOG : Timing DYN 256 +1: [2025-07-31 04:41:58] : LOG : 1.512151 - dyn +1: [2025-07-31 04:41:58] : LOG : 0.000000 - bpm +1: [2025-07-31 04:41:58] : LOG : 0.088926 - bpm_block2 +1: [2025-07-31 04:41:58] : LOG : 0.085212 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 7.16 sec test 2 Start 2: alphabet_utest @@ -4833,9 +4869,9 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 3: Test timeout computed to be: 1500 -3: [2026-09-02 11:01:06] : LOG : Check for correctness. -3: [2026-09-02 11:01:06] : LOG : Timing serial -3: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2025-07-31 04:41:58] : LOG : Check for correctness. +3: [2025-07-31 04:41:58] : LOG : Timing serial +3: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -4843,60 +4879,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 4: Test timeout computed to be: 1500 -4: 371 637 36 803 652 -4: 967 97 417 457 560 -4: 25 612 967 128 261 -4: 96 913 244 785 705 -4: 960 719 649 721 872 -4: 294 908 424 678 44 -4: 616 88 749 724 890 -4: 795 490 997 400 115 -4: 110 627 172 215 897 -4: 206 85 633 951 294 -4: 348 59 790 652 311 -4: 272 760 245 633 957 -4: 40 871 293 143 669 -4: 16 930 888 297 812 -4: 638 743 643 585 855 -4: 883 226 770 29 271 -4: 947 262 54 516 644 -4: 46 897 974 289 991 -4: 779 697 958 666 968 -4: 511 290 872 234 58 -4: 36 11 894 71 470 -4: 595 154 884 650 849 -4: 496 516 109 479 727 -4: 888 901 702 626 723 -4: 491 175 792 739 66 -4: 571 764 816 112 903 -4: 493 34 999 368 618 -4: 342 80 63 867 379 -4: 601 838 866 967 629 -4: 548 604 765 488 136 -4: 376 878 478 612 584 -4: 111 143 339 323 261 -4: 139 567 308 283 139 -4: 609 49 238 974 603 -4: 190 321 259 589 968 -4: 893 376 457 904 96 -4: 691 411 328 13 783 -4: 278 310 367 883 904 -4: 951 270 341 914 520 -4: 418 156 285 35 964 -4: 8 673 804 464 198 -4: 684 202 976 742 268 -4: 537 501 773 751 327 -4: 489 296 864 988 109 -4: 620 15 665 101 171 -4: 84 810 334 467 843 -4: 706 242 32 224 870 -4: 576 911 329 899 998 -4: 387 78 107 85 719 -4: 202 283 615 982 802 -4: 93 697 673 793 591 -4: 622 923 455 704 367 -4: 842 899 289 710 882 -4: 939 886 568 512 282 +4: 385 790 951 245 399 +4: 179 366 677 472 878 +4: 861 401 315 703 921 +4: 144 906 956 699 477 +4: 889 872 464 467 392 +4: 47 969 72 306 322 +4: 316 835 941 178 770 +4: 104 40 752 668 529 +4: 845 9 904 287 834 +4: 939 2 158 442 377 +4: 964 488 22 887 227 +4: 389 453 962 113 739 +4: 832 228 204 309 595 +4: 970 317 686 307 892 +4: 436 913 89 612 24 +4: 571 357 691 951 415 +4: 688 982 948 358 979 +4: 278 731 596 754 686 +4: 331 876 994 776 46 +4: 431 491 840 316 73 +4: 543 290 986 379 132 +4: 975 652 829 245 461 +4: 499 994 986 284 58 +4: 481 636 270 2 358 +4: 773 264 301 706 682 +4: 256 18 135 581 481 +4: 191 468 756 1 174 +4: 720 194 933 833 715 +4: 506 284 355 151 836 +4: 908 70 108 527 378 +4: 446 940 358 665 314 +4: 341 760 577 212 233 +4: 925 20 213 744 605 +4: 980 932 409 641 7 +4: 691 232 348 729 461 +4: 483 928 276 15 577 +4: 481 545 220 74 799 +4: 841 639 456 984 562 +4: 380 79 914 787 770 +4: 457 137 45 462 791 +4: 572 299 444 223 242 +4: 566 746 703 634 208 +4: 354 622 942 692 690 +4: 640 482 932 47 657 +4: 161 632 554 651 287 +4: 551 724 151 298 591 +4: 276 133 377 148 586 +4: 405 457 583 752 209 +4: 772 427 290 845 717 +4: 69 709 524 697 884 +4: 3 443 369 901 667 +4: 911 137 830 311 123 +4: 795 862 815 814 79 +4: 816 0 3 352 725 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -4932,15 +4968,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -6: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:01:06] : LOG : Building guide tree. -6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-09-02 11:01:06] : LOG : Aligning -6: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +6: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:58] : LOG : Building guide tree. +6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-07-31 04:41:58] : LOG : Aligning +6: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4976,15 +5012,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -7: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:01:06] : LOG : Building guide tree. -7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-09-02 11:01:06] : LOG : Aligning -7: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +7: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:58] : LOG : Building guide tree. +7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-07-31 04:41:58] : LOG : Aligning +7: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -5020,15 +5056,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -8: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:01:06] : LOG : Building guide tree. -8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-09-02 11:01:06] : LOG : Aligning -8: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +8: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:58] : LOG : Building guide tree. +8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-07-31 04:41:58] : LOG : Aligning +8: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5076,15 +5112,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -9: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:01:06] : LOG : Building guide tree. -9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-09-02 11:01:06] : LOG : Aligning -9: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +9: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:58] : LOG : Building guide tree. +9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-07-31 04:41:58] : LOG : Aligning +9: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5132,15 +5168,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -10: [2026-09-02 11:01:06] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:01:06] : LOG : Building guide tree. -10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-09-02 11:01:06] : LOG : Aligning -10: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +10: [2025-07-31 04:41:58] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:58] : LOG : Building guide tree. +10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-07-31 04:41:58] : LOG : Aligning +10: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5188,15 +5224,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2026-09-02 11:01:06] : LOG : Detected protein sequences. -11: [2026-09-02 11:01:06] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-09-02 11:01:06] : LOG : Calculating pairwise distances -11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2026-09-02 11:01:06] : LOG : Building guide tree. -11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2026-09-02 11:01:06] : LOG : Aligning -11: [2026-09-02 11:01:06] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:58] : LOG : Detected protein sequences. +11: [2025-07-31 04:41:58] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:58] : LOG : Calculating pairwise distances +11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:58] : LOG : Building guide tree. +11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2025-07-31 04:41:58] : LOG : Aligning +11: [2025-07-31 04:41:58] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -5512,29 +5548,29 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2026-09-02 11:01:06] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-09-02 11:01:06] : LOG : Protein alignments - 20 seq +12: [2025-07-31 04:41:58] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-07-31 04:41:58] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 10% 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-09-02 11:01:09] : LOG : Protein alignments - 1000 seq +12: [2025-07-31 04:42:01] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-09-02 11:01:20] : LOG : Protein alignments - 10000 seq +12: [2025-07-31 04:42:12] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2026-09-02 11:01:30] : LOG : DNA alignments - 20 seq +12: [2025-07-31 04:42:21] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% 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] 90% [==================================================] 100% -12: [2026-09-02 11:01:39] : LOG : DNA alignments - 10000 seq +12: [2025-07-31 04:42:30] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 37.09 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 35.94 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 44.46 sec +Total Test time (real) = 43.21 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5602,12 +5638,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2208375/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1867936 and its subdirectories -I: Current time: Tue Sep 1 23:01:51 -12 2026 -I: pbuilder-time-stamp: 1788346911 +I: removing directory /srv/workspace/pbuilder/2208375 and its subdirectories +I: Current time: Thu Jul 31 18:42:50 +14 2025 +I: pbuilder-time-stamp: 1753936970 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/kalign_3.4.0-1.diff: 95.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/kalign_3.4.0-1.diff.gz b2/build.log: 92.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 92.5% -- replaced with stdout Thu Jul 31 04:42:52 UTC 2025 I: diffoscope 302 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_kalign_trixie_amd64_1753936972 + touch /var/log/reproducible-builds/diffoscope_stamp_kalign_trixie_amd64_1753936972 + RESULT=0 + systemd-run '--description=diffoscope on kalign/1:3.4.0-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_6-52134 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ --run-session -c jenkins-reproducible-trixie-diffoscope-718c561a-006a-4c8c-b8f1-18747c01f83b -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/dbd-tmp-6wDJEQF ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1/kalign_3.4.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2/kalign_3.4.0-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_6-52134.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/kalign_3.4.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b1/kalign_3.4.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.u98MuRLQ/b2/kalign_3.4.0-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 160ms CPU time consumed: 162ms _ _ _ | | ____ _| (_) __ _ _ __ | |/ / _` | | |/ _` | '_ \ | < (_| | | | (_| | | | | |_|\_\__,_|_|_|\__, |_| |_| |___/ Thu Jul 31 04:42:53 UTC 2025 I: diffoscope 302 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 31 04:42:53 UTC 2025 I: kalign from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-07-31 04:42:53] INFO: Starting at 2025-07-31 04:42:53.487540 [2025-07-31 04:42:53] INFO: Generating the pages of 1 package(s) [2025-07-31 04:42:53] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/kalign didn't produce a buildlog, even though it has been built. [2025-07-31 04:42:53] INFO: Finished at 2025-07-31 04:42:53.734146, took: 0:00:00.246611 Thu Jul 31 04:42:53 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/kalign.html Thu Jul 31 04:42:53 UTC 2025 I: Removing signed kalign_3.4.0-1_amd64.buildinfo.asc files: removed './b1/kalign_3.4.0-1_amd64.buildinfo.asc' removed './b2/kalign_3.4.0-1_amd64.buildinfo.asc' 1753936973 amd64 trixie kalign Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/kalign_3.4.0-1.rbuild.log: 92.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/kalign_3.4.0-1.rbuild.log.gz [2025-07-31 04:42:54] INFO: Starting at 2025-07-31 04:42:54.041187 [2025-07-31 04:42:54] INFO: Generating the pages of 1 package(s) [2025-07-31 04:42:54] INFO: Finished at 2025-07-31 04:42:54.275928, took: 0:00:00.234747 All cleanup done. Thu Jul 31 04:42:54 UTC 2025 - total duration: 0h 10m 20s. Thu Jul 31 04:42:54 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-iCi7rdze, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 10min 21.365s CPU time consumed: 4.956s