Running as unit: rb-build-arm64_20-38708.service ==================================================================================== Fri Sep 27 03:31:07 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_20) on jenkins, called using "codethink02-arm64 codethink04-arm64" as arguments. Fri Sep 27 03:31:07 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-Au82Iu1u" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 03:31:07 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 03:31:08 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-da6RMX' Fri Sep 27 03:31:08 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Sep 27 03:31:08 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-z6zFqV' ok, let's check if hhsuite is building anywhere yet… ok, hhsuite is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of hhsuite in unstable on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Fri Sep 27 03:31:30 UTC 2024 I: starting to build hhsuite/unstable/arm64 on jenkins on '2024-09-27 03:31' Fri Sep 27 03:31:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/38708/console.log 1727407890 arm64 unstable hhsuite Fri Sep 27 03:31:30 UTC 2024 I: Downloading source for unstable/hhsuite=3.3.0+ds-8 --2024-09-27 03:31:31-- http://deb.debian.org/debian/pool/main/h/hhsuite/hhsuite_3.3.0%2bds-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2271 (2.2K) [text/prs.lines.tag] Saving to: ‘hhsuite_3.3.0+ds-8.dsc’ 0K .. 100% 229M=0s 2024-09-27 03:31:31 (229 MB/s) - ‘hhsuite_3.3.0+ds-8.dsc’ saved [2271/2271] --2024-09-27 03:31:31-- http://deb.debian.org/debian/pool/main/h/hhsuite/hhsuite_3.3.0%2bds-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2271 (2.2K) [text/prs.lines.tag] Saving to: ‘hhsuite_3.3.0+ds-8.dsc’ 0K .. 100% 229M=0s 2024-09-27 03:31:31 (229 MB/s) - ‘hhsuite_3.3.0+ds-8.dsc’ saved [2271/2271] Fri Sep 27 03:31:31 UTC 2024 I: hhsuite_3.3.0+ds-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hhsuite Binary: hhsuite, hhsuite-data Architecture: any all Version: 3.3.0+ds-8 Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille , Sascha Steinbiss Homepage: https://toolkit.tuebingen.mpg.de/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/hhsuite Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man Package-List: hhsuite deb science optional arch=any hhsuite-data deb science optional arch=all Checksums-Sha1: d90462ba593366296d8916e184b42325caa4201b 4775072 hhsuite_3.3.0+ds.orig.tar.xz 0c6aa80d717ee79df31a05f33d2f461b1b6f0c88 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Checksums-Sha256: a81037f2e2a4801f1a42f5aa5939334fe038053d05ceabdc0899fefb8cc00a44 4775072 hhsuite_3.3.0+ds.orig.tar.xz d408a3d42581737068f06b96cd922c462f672beeb4faf94f41ac37340170b3cb 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Files: d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz 81b05abfd099550bfb153063e218961e 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Dgit: 140af672217dfdd27cb9e04f647e16721cab7092 debian archive/debian/3.3.0+ds-8 https://git.dgit.debian.org/hhsuite -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmTYqGkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoEMA/+LuZTmLibgbYZApaOGZdaX+PkhrsA zfcKaSk3+e/HPlWNU154xxOVy+O+Y5pCo/EknRdiMEmQPW4Xp5CJOKEFkJE98rpu zorYV6MrnGZbtce76kYae9bIOO7ufuZgOmJQmC8o4Br1ARVzcdb0CoeT/I/YlUaO 1GeZ7FRxPV5+2FnJepnZtN3pVs9flLqfmjkTUpuXunVczXQ/9OqQDHLl+9FRuW9l G/rWE7wu1PZC12UYSIOaCP5ZLWBdD8aTCrD787zdv7NEdhH19LJmrpNiaV9pUmbn 1gWsCwnOkTJPw49XsA6PmabKG3eigVh/vX9OPCyUIFlwsgWk1j59a6iuRdVfKKec tu6iS43HxaDNpmr9RDMPwRy0IJyzFVVfefcFEkiq81xvXWeCyZaIMZG1jiprbitC n17iBZeZbuSNpVfwA8afeBsxfEQF5mMa14pv0b1tYMxFySu578muNQulSbVHRyIm U1EV7JmoLcrAdNisorrWjHxsreQpWDWoTtttMhQiHGRAqusHl3AfNChpj1VdctFp DLSXPJR57EGgm6Wh/l/dcAsYsoTRxoZwIslbpyajyZLIMgJsBYXU+aQyAnnix+KN OKWs50hmPC09YXC7cia0qp2IlQaR/Si5jpY2nDoxi115qKH1z6k+s49gHHEXcZGP OCf9WhUaFjSQ0Yk= =W1CO -----END PGP SIGNATURE----- Fri Sep 27 03:31:31 UTC 2024 I: Checking whether the package is not for us Fri Sep 27 03:31:31 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Sep 27 03:31:31 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Sep 27 03:31:31 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 03:31:31 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-oDL7kh' ==================================================================================== Fri Sep 27 03:31:32 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 hhsuite unstable /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ 3.3.0+ds-8" as arguments. Fri Sep 27 03:31:32 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-lstJ38Hx" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 03:31:32 UTC 2024 I: Downloading source for unstable/hhsuite=3.3.0+ds-8 Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hhsuite.git Please use: git clone https://salsa.debian.org/med-team/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4794 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (dsc) [2271 B] Get:2 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (tar) [4775 kB] Get:3 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (diff) [16.9 kB] Fetched 4794 kB in 0s (12.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hhsuite.git Please use: git clone https://salsa.debian.org/med-team/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4794 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (dsc) [2271 B] Get:2 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (tar) [4775 kB] Get:3 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (diff) [16.9 kB] Fetched 4794 kB in 0s (12.5 MB/s) Download complete and in download only mode ============================================================================= Building hhsuite in unstable on arm64 on codethink02-arm64 now. Date: Fri Sep 27 04:31:33 BST 2024 Date UTC: Fri Sep 27 03:31:33 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 15:31:34 -12 2024 I: pbuilder-time-stamp: 1727407894 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hhsuite_3.3.0+ds-8.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 13 09:54:49 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting hhsuite in hhsuite-3.3.0+ds dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.3.0+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_without_mpi dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying python3 dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying exe_suffix dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3287051/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8aa3f2c7ca914a479b75daf1ca5462b4' 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='3287051' 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.tpeY5JWQ/pbuilderrc_Uxar --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1 --logfile b1/build.log hhsuite_3.3.0+ds-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3287051/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-6.q16-7t64{a} libmagickwand-6.q16-7t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libraw23t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsimde-dev{a} libssh2-1t64{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{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 fonts-urw-base35 ghostscript krb5-locales libarchive-cpio-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmagickcore-6.q16-7-extra libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 46.3 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-1+b3 [329 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.4.3-1 [251 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.18.2-2 [10.9 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.18.2-2 [14.1 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.18.2-2 [272 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b1 [26.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libraw23t64 arm64 0.21.2-2.1 [366 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1 [67.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libmagickcore-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [1515 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libmagickwand-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [247 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1 [323 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 64 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.10.1-1 [322 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.30.3-1 [2221 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.30.3-1 [9398 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 85 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1 [290 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1 [19.6 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Fetched 46.3 MB in 0s (99.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19897 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../01-libfftw3-double3_3.3.10-1+b3_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-1+b3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../02-libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../03-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../04-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../05-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../08-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../09-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../10-libsharpyuv0_1.4.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... Selecting previously unselected package libdav1d7:arm64. Preparing to unpack .../11-libdav1d7_1.4.3-1_arm64.deb ... Unpacking libdav1d7:arm64 (1.4.3-1) ... Selecting previously unselected package libheif-plugin-dav1d:arm64. Preparing to unpack .../12-libheif-plugin-dav1d_1.18.2-2_arm64.deb ... Unpacking libheif-plugin-dav1d:arm64 (1.18.2-2) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../13-libde265-0_1.0.15-1+b2_arm64.deb ... Unpacking libde265-0:arm64 (1.0.15-1+b2) ... Selecting previously unselected package libheif-plugin-libde265:arm64. Preparing to unpack .../14-libheif-plugin-libde265_1.18.2-2_arm64.deb ... Unpacking libheif-plugin-libde265:arm64 (1.18.2-2) ... Selecting previously unselected package libheif1:arm64. Preparing to unpack .../15-libheif1_1.18.2-2_arm64.deb ... Unpacking libheif1:arm64 (1.18.2-2) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../16-libjbig0_2.1-6.1+b1_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../17-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../18-liblcms2-2_2.14-2+b1_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2+b1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../19-libglib2.0-0t64_2.82.1-1_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.1-1) ... Selecting previously unselected package liblqr-1-0:arm64. Preparing to unpack .../20-liblqr-1-0_0.4.2-2.1+b1_arm64.deb ... Unpacking liblqr-1-0:arm64 (0.4.2-2.1+b1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../21-libltdl7_2.4.7-7+b1_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../22-libopenjp2-7_2.5.0-2+b3_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.0-2+b3) ... Selecting previously unselected package libraw23t64:arm64. Preparing to unpack .../23-libraw23t64_0.21.2-2.1_arm64.deb ... Unpacking libraw23t64:arm64 (0.21.2-2.1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../24-libdeflate0_1.21-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.21-1) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../25-liblerc4_4.0.0+ds-4+b1_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../26-libwebp7_1.4.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../27-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libwebpdemux2:arm64. Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_arm64.deb ... Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_arm64.deb ... Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../30-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../31-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../32-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../33-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../34-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../35-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../36-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../37-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../38-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1_all.deb ... Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1) ... Selecting previously unselected package libmagickcore-6.q16-7t64:arm64. Preparing to unpack .../39-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1_arm64.deb ... Unpacking libmagickcore-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1) ... Selecting previously unselected package libmagickwand-6.q16-7t64:arm64. Preparing to unpack .../40-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1_arm64.deb ... Unpacking libmagickwand-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../41-libproc2-0_2%3a4.0.4-5_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../42-procps_2%3a4.0.4-5_arm64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../43-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../44-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../45-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../46-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../47-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../48-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../49-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../50-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../51-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../52-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../53-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../54-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../55-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../56-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../57-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../58-libarchive13t64_3.7.4-1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../59-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../60-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../61-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../62-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../63-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../64-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../65-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../66-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../67-libldap-2.5-0_2.5.18+dfsg-3_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../68-libnghttp2-14_1.63.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.63.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../69-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../70-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../71-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../72-libcurl4t64_8.10.1-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.10.1-1) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../73-libjsoncpp25_1.9.5-6+b2_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../74-librhash0_1.4.3-3+b1_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../75-libuv1t64_1.48.0-6_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-6) ... Selecting previously unselected package cmake-data. Preparing to unpack .../76-cmake-data_3.30.3-1_all.deb ... Unpacking cmake-data (3.30.3-1) ... Selecting previously unselected package cmake. Preparing to unpack .../77-cmake_3.30.3-1_arm64.deb ... Unpacking cmake (3.30.3-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../78-libdebhelper-perl_13.20_all.deb ... 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Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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/aarch64-linux-gnu -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. 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CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. 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Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 5%] Generating ../generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 8%] Generating ../generated/context_data.lib.h [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 11%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 12%] Generating ../generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 14%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 14%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc [ 17%] Linking C executable ffindex_apply cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 18%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 21%] Linking C executable ffindex_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 22%] Linking C executable ffindex_build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 23%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 27%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a [ 28%] Linking CXX static library libhhviterbialgorithm_and_ss.a [ 29%] Linking C executable ffindex_get cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a [ 30%] Linking C executable ffindex_unpack cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 [ 30%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" [ 31%] Linking C executable ffindex_modify /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 31%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend [ 31%] Built target hhviterbialgorithm_and_ss [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 32%] Built target ffindex_unpack make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 33%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 34%] Built target ffindex_modify [ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 36%] Linking C executable ffindex_order make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 36%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake "--color=" [ 36%] Built target hhviterbialgorithm_with_celloff make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 39%] Built target ffindex_order [ 40%] Linking C executable ffindex_from_fasta_with_split [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 42%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 42%] Built target ffindex_from_fasta_with_split [ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp [ 43%] Built target hhviterbialgorithm_with_celloff_and_ss cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 44%] Linking CXX executable a3m_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 45%] Linking CXX static library libCS_OBJECTS.a [ 46%] Linking CXX executable a3m_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 [ 46%] Built target a3m_extract /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 47%] Linking CXX executable a3m_database_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 [ 48%] Linking CXX executable a3m_database_filter [ 48%] Built target CS_OBJECTS cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 48%] Built target a3m_reduce make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 48%] Built target a3m_database_reduce make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 49%] Linking CXX executable a3m_database_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 [ 49%] Built target a3m_database_filter cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 49%] Built target a3m_database_extract make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 49%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP 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src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP 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-Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && 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src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function 'int sprintf(char*, const char*, ...)', inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild 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-I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 89%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp [ 90%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 91%] Linking CXX executable hhblits cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 91%] Built target hhblits [ 92%] Linking CXX executable hhblits_ca3m cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 93%] Linking CXX executable hhalign cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ [ 94%] Linking CXX executable hhalign_omp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable hhsearch make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 95%] Built target hhblits_ca3m [ 96%] Linking CXX executable hhmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 [ 97%] Linking CXX executable hhblits_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Linking CXX executable hhsearch_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhalign_omp [ 99%] Linking CXX executable hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Linking CXX executable hhconsensus cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 [100%] Built target hhalign /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhmake [100%] Built target hhsearch make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhsearch_omp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhconsensus make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_omp [100%] Linking CXX executable cstranslate cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Nothing to be done for 'data/CMakeFiles/generated.dir/build'. make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh - 03:33:49.844 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:50.321 INFO: Alternative alignment: 0 - 03:33:50.335 INFO: 1 alignments done - 03:33:50.368 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:33:50 2024 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) query.a3m 0 32127 322 0 query.a3m 0 32666 18 0 query.a3m 0 32666 171 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 03:33:52.084 INFO: Searching 1 column state sequences. - 03:33:52.184 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:52.202 INFO: Iteration 1 - 03:33:52.765 INFO: Prefiltering database - 03:33:53.292 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:33:53.300 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:33:53.301 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:33:53.301 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:53.370 INFO: Alternative alignment: 0 - 03:33:53.384 INFO: 1 alignments done - 03:33:53.385 INFO: Alternative alignment: 1 - 03:33:53.396 INFO: 1 alignments done - 03:33:53.397 INFO: Alternative alignment: 2 - 03:33:53.397 INFO: Alternative alignment: 3 - 03:33:54.041 INFO: Premerge done - 03:33:54.042 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:54.071 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.27431 Searched_HMMs 1 Date Fri Sep 27 03:33:54 2024 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:33:54.098 INFO: Searching 1 column state sequences. - 03:33:54.210 INFO: Thread 0 query.a3m - 03:33:54.221 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:54.238 INFO: Iteration 1 - 03:33:54.949 INFO: Prefiltering database - 03:33:56.082 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:33:56.088 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:33:56.089 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:33:56.089 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:56.127 INFO: Alternative alignment: 0 - 03:33:56.139 INFO: 1 alignments done - 03:33:56.144 INFO: Alternative alignment: 1 - 03:33:56.155 INFO: 1 alignments done - 03:33:56.156 INFO: Alternative alignment: 2 - 03:33:56.160 INFO: Alternative alignment: 3 - 03:33:56.898 INFO: Premerge done - 03:33:56.900 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:56.930 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 03:33:57.103 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:57.132 INFO: Searching 1 database HHMs without prefiltering - 03:33:57.133 INFO: Iteration 1 - 03:33:57.629 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:57.698 INFO: Alternative alignment: 0 - 03:33:57.711 INFO: 1 alignments done - 03:33:57.711 INFO: Alternative alignment: 1 - 03:33:57.720 INFO: 1 alignments done - 03:33:57.720 INFO: Alternative alignment: 2 - 03:33:57.720 INFO: Alternative alignment: 3 - 03:33:58.187 INFO: Premerge done - 03:33:58.187 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:58.217 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:33:58 2024 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:33:58.336 INFO: Thread 0 query.a3m - 03:33:58.355 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:58.382 INFO: Searching 1 database HHMs without prefiltering - 03:33:58.383 INFO: Iteration 1 - 03:33:59.487 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:59.524 INFO: Alternative alignment: 0 - 03:33:59.535 INFO: 1 alignments done - 03:33:59.540 INFO: Alternative alignment: 1 - 03:33:59.547 INFO: 1 alignments done - 03:33:59.548 INFO: Alternative alignment: 2 - 03:33:59.548 INFO: Alternative alignment: 3 - 03:34:00.602 INFO: Premerge done - 03:34:00.608 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:34:00.644 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild cd mybuild && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_installman -Nhhsuite dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3287051 and its subdirectories I: Current time: Thu Sep 26 15:35:09 -12 2024 I: pbuilder-time-stamp: 1727408109 Fri Sep 27 03:35:09 UTC 2024 I: Signing ./b1/hhsuite_3.3.0+ds-8_arm64.buildinfo as hhsuite_3.3.0+ds-8_arm64.buildinfo.asc Fri Sep 27 03:35:09 UTC 2024 I: Signed ./b1/hhsuite_3.3.0+ds-8_arm64.buildinfo as ./b1/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc Fri Sep 27 03:35:09 UTC 2024 - build #1 for hhsuite/unstable/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Fri Sep 27 03:35:09 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-lstJ38Hx, removing. /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 03:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 03:31 b2 -rw-r--r-- 1 jenkins jenkins 2271 Aug 13 2023 hhsuite_3.3.0+ds-8.dsc -rw------- 1 jenkins jenkins 3398 Sep 27 03:31 rbuildlog.QLwDDTK /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1: total 34364 -rw-r--r-- 1 jenkins jenkins 210534 Sep 27 03:35 build.log -rw-r--r-- 1 jenkins jenkins 4402152 Sep 27 03:35 hhsuite-data_3.3.0+ds-8_all.deb -rw-r--r-- 1 jenkins jenkins 20088632 Sep 27 03:35 hhsuite-dbgsym_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 16868 Sep 27 03:35 hhsuite_3.3.0+ds-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2271 Sep 27 03:35 hhsuite_3.3.0+ds-8.dsc -rw-r--r-- 1 jenkins jenkins 7467 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8349 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1888 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 10426248 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1343 Sep 27 03:35 hhsuite_3.3.0+ds-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2: total 0 Fri Sep 27 03:35:11 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 15:31:34 -12 2024 I: pbuilder-time-stamp: 1727407894 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hhsuite_3.3.0+ds-8.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 13 09:54:49 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting hhsuite in hhsuite-3.3.0+ds dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.3.0+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_without_mpi dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying python3 dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying exe_suffix dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3287051/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8aa3f2c7ca914a479b75daf1ca5462b4' 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='3287051' 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.tpeY5JWQ/pbuilderrc_Uxar --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1 --logfile b1/build.log hhsuite_3.3.0+ds-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3287051/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-6.q16-7t64{a} libmagickwand-6.q16-7t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libraw23t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsimde-dev{a} libssh2-1t64{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{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 fonts-urw-base35 ghostscript krb5-locales libarchive-cpio-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmagickcore-6.q16-7-extra libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 46.3 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-1+b3 [329 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.4.3-1 [251 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.18.2-2 [10.9 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.18.2-2 [14.1 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.18.2-2 [272 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b1 [26.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libraw23t64 arm64 0.21.2-2.1 [366 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1 [67.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libmagickcore-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [1515 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libmagickwand-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [247 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1 [323 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 64 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.10.1-1 [322 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.30.3-1 [2221 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.30.3-1 [9398 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 85 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1 [290 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1 [19.6 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Fetched 46.3 MB in 0s (99.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19897 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../01-libfftw3-double3_3.3.10-1+b3_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-1+b3) ... Selecting previously unselected package libexpat1:arm64. 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Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../61-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../62-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../63-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../64-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../65-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../66-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../67-libldap-2.5-0_2.5.18+dfsg-3_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../68-libnghttp2-14_1.63.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.63.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../69-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../70-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../71-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl4t64:arm64. 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Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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/aarch64-linux-gnu -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. 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CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. 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'/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 5%] Generating ../generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 8%] Generating ../generated/context_data.lib.h [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 11%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 12%] Generating ../generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 14%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 14%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc [ 17%] Linking C executable ffindex_apply cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 18%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 21%] Linking C executable ffindex_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 22%] Linking C executable ffindex_build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 23%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 27%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a [ 28%] Linking CXX static library libhhviterbialgorithm_and_ss.a [ 29%] Linking C executable ffindex_get cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a [ 30%] Linking C executable ffindex_unpack cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 [ 30%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" [ 31%] Linking C executable ffindex_modify /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 31%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend [ 31%] Built target hhviterbialgorithm_and_ss [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 32%] Built target ffindex_unpack make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 33%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 34%] Built target ffindex_modify [ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 36%] Linking C executable ffindex_order make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 36%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake "--color=" [ 36%] Built target hhviterbialgorithm_with_celloff make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 39%] Built target ffindex_order [ 40%] Linking C executable ffindex_from_fasta_with_split [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 42%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 42%] Built target ffindex_from_fasta_with_split [ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp [ 43%] Built target hhviterbialgorithm_with_celloff_and_ss cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 44%] Linking CXX executable a3m_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 45%] Linking CXX static library libCS_OBJECTS.a [ 46%] Linking CXX executable a3m_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 [ 46%] Built target a3m_extract /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 47%] Linking CXX executable a3m_database_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 [ 48%] Linking CXX executable a3m_database_filter [ 48%] Built target CS_OBJECTS cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 48%] Built target a3m_reduce make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 48%] Built target a3m_database_reduce make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 49%] Linking CXX executable a3m_database_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 [ 49%] Built target a3m_database_filter cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 49%] Built target a3m_database_extract make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 49%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP 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src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP 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-Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function 'int sprintf(char*, const char*, ...)', inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild 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make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build [ 80%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 81%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o [ 82%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated 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-I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfilter.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make 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-mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 84%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build [ 86%] Building CXX object src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhconsensus.cpp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 87%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o 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-I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 89%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp [ 90%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 91%] Linking CXX executable hhblits cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 91%] Built target hhblits [ 92%] Linking CXX executable hhblits_ca3m cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 93%] Linking CXX executable hhalign cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ [ 94%] Linking CXX executable hhalign_omp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable hhsearch make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 95%] Built target hhblits_ca3m [ 96%] Linking CXX executable hhmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 [ 97%] Linking CXX executable hhblits_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Linking CXX executable hhsearch_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhalign_omp [ 99%] Linking CXX executable hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Linking CXX executable hhconsensus cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 [100%] Built target hhalign /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhmake [100%] Built target hhsearch make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhsearch_omp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhconsensus make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_omp [100%] Linking CXX executable cstranslate cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Nothing to be done for 'data/CMakeFiles/generated.dir/build'. make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh - 03:33:49.844 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:50.321 INFO: Alternative alignment: 0 - 03:33:50.335 INFO: 1 alignments done - 03:33:50.368 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:33:50 2024 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) query.a3m 0 32127 322 0 query.a3m 0 32666 18 0 query.a3m 0 32666 171 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 03:33:52.084 INFO: Searching 1 column state sequences. - 03:33:52.184 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:52.202 INFO: Iteration 1 - 03:33:52.765 INFO: Prefiltering database - 03:33:53.292 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:33:53.300 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:33:53.301 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:33:53.301 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:53.370 INFO: Alternative alignment: 0 - 03:33:53.384 INFO: 1 alignments done - 03:33:53.385 INFO: Alternative alignment: 1 - 03:33:53.396 INFO: 1 alignments done - 03:33:53.397 INFO: Alternative alignment: 2 - 03:33:53.397 INFO: Alternative alignment: 3 - 03:33:54.041 INFO: Premerge done - 03:33:54.042 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:54.071 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.27431 Searched_HMMs 1 Date Fri Sep 27 03:33:54 2024 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:33:54.098 INFO: Searching 1 column state sequences. - 03:33:54.210 INFO: Thread 0 query.a3m - 03:33:54.221 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:54.238 INFO: Iteration 1 - 03:33:54.949 INFO: Prefiltering database - 03:33:56.082 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:33:56.088 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:33:56.089 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:33:56.089 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:56.127 INFO: Alternative alignment: 0 - 03:33:56.139 INFO: 1 alignments done - 03:33:56.144 INFO: Alternative alignment: 1 - 03:33:56.155 INFO: 1 alignments done - 03:33:56.156 INFO: Alternative alignment: 2 - 03:33:56.160 INFO: Alternative alignment: 3 - 03:33:56.898 INFO: Premerge done - 03:33:56.900 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:56.930 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 03:33:57.103 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:57.132 INFO: Searching 1 database HHMs without prefiltering - 03:33:57.133 INFO: Iteration 1 - 03:33:57.629 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:57.698 INFO: Alternative alignment: 0 - 03:33:57.711 INFO: 1 alignments done - 03:33:57.711 INFO: Alternative alignment: 1 - 03:33:57.720 INFO: 1 alignments done - 03:33:57.720 INFO: Alternative alignment: 2 - 03:33:57.720 INFO: Alternative alignment: 3 - 03:33:58.187 INFO: Premerge done - 03:33:58.187 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:33:58.217 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:33:58 2024 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:33:58.336 INFO: Thread 0 query.a3m - 03:33:58.355 INFO: query.a3m is in A2M, A3M or FASTA format - 03:33:58.382 INFO: Searching 1 database HHMs without prefiltering - 03:33:58.383 INFO: Iteration 1 - 03:33:59.487 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:33:59.524 INFO: Alternative alignment: 0 - 03:33:59.535 INFO: 1 alignments done - 03:33:59.540 INFO: Alternative alignment: 1 - 03:33:59.547 INFO: 1 alignments done - 03:33:59.548 INFO: Alternative alignment: 2 - 03:33:59.548 INFO: Alternative alignment: 3 - 03:34:00.602 INFO: Premerge done - 03:34:00.608 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:34:00.644 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild cd mybuild && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_installman -Nhhsuite dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3287051 and its subdirectories I: Current time: Thu Sep 26 15:35:09 -12 2024 I: pbuilder-time-stamp: 1727408109 Fri Sep 27 03:35:12 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Sep 27 03:35:12 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Sep 27 03:35:12 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Sep 27 03:35:12 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-VGhBIm' ==================================================================================== Fri Sep 27 03:35:13 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 hhsuite unstable /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ 3.3.0+ds-8" as arguments. Fri Sep 27 03:35:13 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-0JjBRnPw" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 03:35:14 UTC 2024 I: Downloading source for unstable/hhsuite=3.3.0+ds-8 Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hhsuite.git Please use: git clone https://salsa.debian.org/med-team/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4794 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (dsc) [2271 B] Get:2 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (tar) [4775 kB] Get:3 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (diff) [16.9 kB] Fetched 4794 kB in 0s (73.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hhsuite.git Please use: git clone https://salsa.debian.org/med-team/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4794 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (dsc) [2271 B] Get:2 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (tar) [4775 kB] Get:3 http://deb.debian.org/debian unstable/main hhsuite 3.3.0+ds-8 (diff) [16.9 kB] Fetched 4794 kB in 0s (73.5 MB/s) Download complete and in download only mode ============================================================================= Re-Building hhsuite in unstable on arm64 on codethink04-arm64 now. Date: Fri Sep 27 04:35:14 BST 2024 Date UTC: Fri Sep 27 03:35:14 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/pbuilderrc_jr59 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' hhsuite = debian-installer -o hhsuite = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' hhsuite = u-boot ']' + case "${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.tpeY5JWQ/pbuilderrc_jr59 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2 --logfile b2/build.log hhsuite_3.3.0+ds-8.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: Fri Sep 27 17:35:14 +14 2024 I: pbuilder-time-stamp: 1727408114 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hhsuite_3.3.0+ds-8.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 13 09:54:49 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting hhsuite in hhsuite-3.3.0+ds dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.3.0+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_without_mpi dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying python3 dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying exe_suffix dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. 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 Sep 27 03:35 /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/1173700/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1173700/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=2bab0760e8bc4a32b942d996d981533b LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=1173700 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.tpeY5JWQ/pbuilderrc_jr59 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2 --logfile b2/build.log hhsuite_3.3.0+ds-8.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-6.q16-7t64{a} libmagickwand-6.q16-7t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libraw23t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsimde-dev{a} libssh2-1t64{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{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 fonts-urw-base35 ghostscript krb5-locales libarchive-cpio-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmagickcore-6.q16-7-extra libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 46.3 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-1+b3 [329 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.4.3-1 [251 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.18.2-2 [10.9 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.18.2-2 [14.1 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.18.2-2 [272 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b1 [26.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libraw23t64 arm64 0.21.2-2.1 [366 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1 [67.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libmagickcore-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [1515 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libmagickwand-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1 [247 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1 [323 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 64 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.10.1-1 [322 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.30.3-1 [2221 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.30.3-1 [9398 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 85 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1 [290 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1 [19.6 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Fetched 46.3 MB in 0s (170 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19897 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../01-libfftw3-double3_3.3.10-1+b3_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-1+b3) ... Selecting previously unselected package libexpat1:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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/aarch64-linux-gnu -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (3.6s) -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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/aarch64-linux-gnu -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP -- Configuring done (1.1s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild cd mybuild && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds 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src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 7%] Generating ../generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated [ 9%] Generating ../generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 14%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 14%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 19%] Linking C executable ffindex_apply cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a [ 20%] Linking C executable ffindex_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 20%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 20%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build [ 22%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 24%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend [ 25%] Linking C executable ffindex_get make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 26%] Linking C executable ffindex_build /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 28%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 28%] Built target ffindex_get make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild 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/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd 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'/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 31%] Built target ffindex_from_fasta make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Linking CXX static library libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake [ 37%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" [ 37%] Built target ffindex_order make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 [ 38%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 41%] Linking C executable ffindex_from_fasta_with_split cd 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'/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 41%] Built target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" [ 41%] Built target ffindex_from_fasta_with_split [ 41%] Built target hhviterbialgorithm_and_ss [ 42%] Linking CXX static library libCS_OBJECTS.a [ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Built target CS_OBJECTS [ 44%] Built target hhviterbialgorithm_with_celloff_and_ss cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build [ 46%] Linking CXX executable a3m_reduce [ 45%] Linking CXX executable a3m_extract make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 53%] Built target a3m_extract make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 54%] Linking CXX executable a3m_database_extract [ 55%] Linking CXX executable a3m_database_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 [ 55%] Built target a3m_reduce [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhutil.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 57%] 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-Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function 'int sprintf(char*, const char*, ...)', inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make -f 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directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[4]: Leaving directory 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'/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 80%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake.dir/hhmake.cpp.o -MF CMakeFiles/hhmake.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmake.cpp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' 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-Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 87%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o [ 88%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 89%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 90%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 91%] Linking CXX executable hhalign cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 [ 92%] Linking CXX executable hhblits cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 93%] Linking CXX executable hhsearch cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 93%] Built target hhalign [ 94%] Linking CXX executable hhsearch_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 94%] Built target hhblits /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable hhblits_ca3m cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 95%] Built target hhsearch [ 96%] Linking CXX executable hhblits_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 96%] Built target hhsearch_omp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 96%] Built target hhblits_ca3m [ 97%] Linking CXX executable hhmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 97%] Built target hhblits_omp [ 98%] Linking CXX executable hhconsensus cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhmake make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhconsensus /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX executable hhalign_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [100%] Linking CXX executable hhfilter cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhalign_omp [100%] Linking CXX executable cstranslate cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Nothing to be done for 'data/CMakeFiles/generated.dir/build'. make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh - 03:36:49.960 INFO: query.a3m is in A2M, A3M or FASTA format - 03:36:50.348 INFO: Alternative alignment: 0 - 03:36:50.356 INFO: 1 alignments done - 03:36:50.375 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:36:50 2024 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) query.a3m 0 32127 286 0 query.a3m 0 32666 5 0 query.a3m 0 32666 100 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 03:36:51.570 INFO: Searching 1 column state sequences. - 03:36:51.633 INFO: query.a3m is in A2M, A3M or FASTA format - 03:36:51.649 INFO: Iteration 1 - 03:36:52.050 INFO: Prefiltering database - 03:36:52.332 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:36:52.333 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:36:52.333 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:36:52.333 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:36:52.373 INFO: Alternative alignment: 0 - 03:36:52.379 INFO: 1 alignments done - 03:36:52.379 INFO: Alternative alignment: 1 - 03:36:52.386 INFO: 1 alignments done - 03:36:52.386 INFO: Alternative alignment: 2 - 03:36:52.386 INFO: Alternative alignment: 3 - 03:36:52.757 INFO: Premerge done - 03:36:52.758 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:36:52.785 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.27431 Searched_HMMs 1 Date Fri Sep 27 03:36:52 2024 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:36:52.808 INFO: Searching 1 column state sequences. - 03:36:52.867 INFO: Thread 0 query.a3m - 03:36:52.878 INFO: query.a3m is in A2M, A3M or FASTA format - 03:36:52.895 INFO: Iteration 1 - 03:36:53.426 INFO: Prefiltering database - 03:36:53.951 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 03:36:53.951 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 03:36:53.951 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 03:36:53.951 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:36:53.970 INFO: Alternative alignment: 0 - 03:36:53.977 INFO: 1 alignments done - 03:36:53.977 INFO: Alternative alignment: 1 - 03:36:53.984 INFO: 1 alignments done - 03:36:53.984 INFO: Alternative alignment: 2 - 03:36:53.984 INFO: Alternative alignment: 3 - 03:36:54.545 INFO: Premerge done - 03:36:54.545 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:36:54.565 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 03:36:54.653 INFO: query.a3m is in A2M, A3M or FASTA format - 03:36:54.669 INFO: Searching 1 database HHMs without prefiltering - 03:36:54.669 INFO: Iteration 1 - 03:36:54.990 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:36:55.028 INFO: Alternative alignment: 0 - 03:36:55.035 INFO: 1 alignments done - 03:36:55.035 INFO: Alternative alignment: 1 - 03:36:55.042 INFO: 1 alignments done - 03:36:55.042 INFO: Alternative alignment: 2 - 03:36:55.042 INFO: Alternative alignment: 3 - 03:36:55.411 INFO: Premerge done - 03:36:55.411 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:36:55.441 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 Date Fri Sep 27 03:36:55 2024 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) - 03:36:55.524 INFO: Thread 0 query.a3m - 03:36:55.536 INFO: query.a3m is in A2M, A3M or FASTA format - 03:36:55.552 INFO: Searching 1 database HHMs without prefiltering - 03:36:55.552 INFO: Iteration 1 - 03:36:56.079 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 03:36:56.098 INFO: Alternative alignment: 0 - 03:36:56.105 INFO: 1 alignments done - 03:36:56.105 INFO: Alternative alignment: 1 - 03:36:56.111 INFO: 1 alignments done - 03:36:56.111 INFO: Alternative alignment: 2 - 03:36:56.111 INFO: Alternative alignment: 3 - 03:36:56.674 INFO: Premerge done - 03:36:56.674 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 03:36:56.697 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild cd mybuild && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j12 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_installman -Nhhsuite dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1173700/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/1173700 and its subdirectories I: Current time: Fri Sep 27 17:37:51 +14 2024 I: pbuilder-time-stamp: 1727408271 + false + set +x Fri Sep 27 03:37:51 UTC 2024 I: Signing ./b2/hhsuite_3.3.0+ds-8_arm64.buildinfo as hhsuite_3.3.0+ds-8_arm64.buildinfo.asc Fri Sep 27 03:37:51 UTC 2024 I: Signed ./b2/hhsuite_3.3.0+ds-8_arm64.buildinfo as ./b2/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc Fri Sep 27 03:37:51 UTC 2024 - build #2 for hhsuite/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Sep 27 03:37:51 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-0JjBRnPw, removing. /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ: total 228 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 03:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 03:37 b2 -rw-r--r-- 1 jenkins jenkins 2271 Aug 13 2023 hhsuite_3.3.0+ds-8.dsc -rw------- 1 jenkins jenkins 214233 Sep 27 03:35 rbuildlog.QLwDDTK /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1: total 34420 -rw-r--r-- 1 jenkins jenkins 210534 Sep 27 03:35 build.log -rw-r--r-- 1 jenkins jenkins 4402152 Sep 27 03:35 hhsuite-data_3.3.0+ds-8_all.deb -rw-r--r-- 1 jenkins jenkins 20088632 Sep 27 03:35 hhsuite-dbgsym_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 16868 Sep 27 03:35 hhsuite_3.3.0+ds-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2271 Sep 27 03:35 hhsuite_3.3.0+ds-8.dsc -rw-r--r-- 1 jenkins jenkins 7467 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8349 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1888 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 10426248 Sep 27 03:35 hhsuite_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1343 Sep 27 03:35 hhsuite_3.3.0+ds-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2: total 34364 -rw-r--r-- 1 jenkins jenkins 212477 Sep 27 03:37 build.log -rw-r--r-- 1 jenkins jenkins 4402152 Sep 27 03:37 hhsuite-data_3.3.0+ds-8_all.deb -rw-r--r-- 1 jenkins jenkins 20088632 Sep 27 03:37 hhsuite-dbgsym_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 16868 Sep 27 03:37 hhsuite_3.3.0+ds-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2271 Sep 27 03:37 hhsuite_3.3.0+ds-8.dsc -rw-r--r-- 1 jenkins jenkins 7467 Sep 27 03:37 hhsuite_3.3.0+ds-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8349 Sep 27 03:37 hhsuite_3.3.0+ds-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1888 Sep 27 03:37 hhsuite_3.3.0+ds-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 10426248 Sep 27 03:37 hhsuite_3.3.0+ds-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1343 Sep 27 03:37 hhsuite_3.3.0+ds-8_source.changes Fri Sep 27 03:37:54 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Sep 27 03:37:55 UTC 2024 I: hhsuite_3.3.0+ds-8_arm64.changes: Format: 1.8 Date: Sun, 13 Aug 2023 10:47:11 +0200 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: all arm64 Version: 3.3.0+ds-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: hhsuite - sensitive protein sequence searching based on HMM-HMM alignment hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment ( Closes: 1037689 Changes: hhsuite (3.3.0+ds-8) unstable; urgency=medium . * Team upload. * gcc-13.patch: new: fix ftbfs with gcc 13. (Closes: #1037689) * d/control: declare compliance to standards version 4.6.2. Checksums-Sha1: 262e7be5b83dc9c81fc3723d97e7a6f2828ad07f 4402152 hhsuite-data_3.3.0+ds-8_all.deb 9b5f1232c913f2d1340bd4bf688b4bb5f08b42cc 20088632 hhsuite-dbgsym_3.3.0+ds-8_arm64.deb 60890a891a40d2180940cb244c8b0cf8b0fd4ebf 7467 hhsuite_3.3.0+ds-8_arm64.buildinfo e5426425160d525cd72de9f975c0b551046f81f2 10426248 hhsuite_3.3.0+ds-8_arm64.deb Checksums-Sha256: a63b9845bb3133774e061b97e68ea55d257a970f86cf588d8f4f3123558839a5 4402152 hhsuite-data_3.3.0+ds-8_all.deb 3c328e2372dbbfbef795ecb51c2b7a3aa3ee8b701d3d5131acbe69efc09dc57a 20088632 hhsuite-dbgsym_3.3.0+ds-8_arm64.deb 6538903945cffb5997c3945bbc47a08e5ff9017d8b8a6db33b6f99ad7e0590bf 7467 hhsuite_3.3.0+ds-8_arm64.buildinfo 89ba245c0a0d7c5a9a34cddbf4f46ff1c2042cff65768ee573b6e51f286194e9 10426248 hhsuite_3.3.0+ds-8_arm64.deb Files: c9b8c4baaf198c024d9f15d0e5ed4ffa 4402152 science optional hhsuite-data_3.3.0+ds-8_all.deb 49deb43f94d6936e424d5dfef115ac5d 20088632 debug optional hhsuite-dbgsym_3.3.0+ds-8_arm64.deb ae6ee3ff908c44d5328d6025393df9a5 7467 science optional hhsuite_3.3.0+ds-8_arm64.buildinfo 6aaad98724bd430e565722796d0e06d5 10426248 science optional hhsuite_3.3.0+ds-8_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hhsuite_3.3.0+ds-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hhsuite_3.3.0+ds-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hhsuite_3.3.0+ds-8.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hhsuite_3.3.0+ds-8.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/hhsuite_3.3.0+ds-8_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hhsuite_3.3.0+ds-8.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-27 03:35:10.756231435 +0000 +++ b2/build.log 2024-09-27 03:37:52.641343185 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 26 15:31:34 -12 2024 -I: pbuilder-time-stamp: 1727407894 +I: Current time: Fri Sep 27 17:35:14 +14 2024 +I: pbuilder-time-stamp: 1727408114 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3287051/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +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 Sep 27 03:35 /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/1173700/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1173700/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='8aa3f2c7ca914a479b75daf1ca5462b4' - 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='3287051' - PS1='# ' - PS2='> ' + INVOCATION_ID=2bab0760e8bc4a32b942d996d981533b + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=1173700 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.tpeY5JWQ/pbuilderrc_Uxar --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1 --logfile b1/build.log hhsuite_3.3.0+ds-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.tpeY5JWQ/pbuilderrc_jr59 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2 --logfile b2/build.log hhsuite_3.3.0+ds-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3287051/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -219,7 +251,7 @@ Get: 93 http://deb.debian.org/debian unstable/main arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1 [290 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1 [19.6 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] -Fetched 46.3 MB in 0s (99.2 MB/s) +Fetched 46.3 MB in 0s (170 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19897 files and directories currently installed.) @@ -637,7 +669,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes +I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable @@ -702,7 +738,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (4.3s) +-- Configuring done (3.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -744,7 +780,7 @@ -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP --- Configuring done (1.7s) +-- Configuring done (1.1s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' @@ -758,85 +794,80 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend +make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" -[ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -[ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c -[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -[ 5%] Generating ../generated/context_data.crf.h +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 1%] Generating ../generated/context_data.crf.h +[ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated +[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +[ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -[ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +[ 7%] Generating ../generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 8%] Generating ../generated/context_data.lib.h -[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +[ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp 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-mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc -[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc -[ 11%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp -[ 12%] Generating ../generated/cs219.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc -[ 14%] Linking C static library libffindex.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 -/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o -/usr/bin/ranlib libffindex.a /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); @@ -852,6 +883,11 @@ /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ +[ 14%] Linking C static library libffindex.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 +/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o +/usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 14%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend @@ -862,260 +898,260 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c +[ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc +[ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld -[ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc -[ 17%] Linking C executable ffindex_apply -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" -[ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 18%] Built target ffindex_apply +[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c +[ 19%] Linking C executable ffindex_apply +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a +[ 20%] Linking C executable ffindex_reduce +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 20%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" -[ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c -[ 21%] Linking C executable ffindex_reduce -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 22%] Linking C executable ffindex_build -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 -[ 22%] Built target ffindex_reduce +[ 20%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a +[ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +[ 22%] Linking CXX static library libA3M_COMPRESS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c -[ 23%] Built target ffindex_build +[ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c +/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +/usr/bin/ranlib libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 24%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend +[ 25%] Linking C executable ffindex_get make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 26%] Linking C executable ffindex_build +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a +[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build -[ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c -[ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c -[ 27%] Linking C executable ffindex_from_fasta +[ 28%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a -[ 28%] Linking CXX static library libhhviterbialgorithm_and_ss.a -[ 29%] Linking C executable ffindex_get -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a -[ 30%] Linking C executable ffindex_unpack -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -[ 30%] Built target ffindex_from_fasta +[ 28%] Built target ffindex_get +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" -[ 31%] Linking C executable ffindex_modify -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a +[ 29%] Built target ffindex_build +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend +[ 30%] Linking C executable ffindex_modify +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a +[ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 31%] Built target ffindex_get -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend -[ 31%] Built target hhviterbialgorithm_and_ss -[ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 32%] Built target ffindex_unpack -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 31%] Built target ffindex_from_fasta make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 33%] Linking CXX static library libA3M_COMPRESS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake -[ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c -[ 34%] Built target ffindex_modify -[ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libA3M_COMPRESS.a -/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 36%] Linking C executable ffindex_order -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -[ 36%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a +[ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake "--color=" +[ 32%] Built target ffindex_modify +[ 33%] Linking C executable ffindex_unpack +make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake "--color=" -[ 36%] Built target hhviterbialgorithm_with_celloff -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build +[ 34%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 35%] Linking C executable ffindex_order +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a +[ 36%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 37%] Linking CXX static library libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +[ 37%] Built target ffindex_unpack +make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" +[ 37%] Built target ffindex_order +make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 +[ 38%] Linking CXX static library libhhviterbialgorithm_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 37%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp -[ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -[ 39%] Built target ffindex_order -[ 40%] Linking C executable ffindex_from_fasta_with_split -[ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 +[ 40%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -[ 42%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp +/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 41%] Linking C executable ffindex_from_fasta_with_split +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 +/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 42%] Built target ffindex_from_fasta_with_split +[ 41%] Built target hhviterbialgorithm_with_celloff +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" +[ 41%] Built target ffindex_from_fasta_with_split +[ 41%] Built target hhviterbialgorithm_and_ss +[ 42%] Linking CXX static library libCS_OBJECTS.a [ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 -/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp -[ 43%] Built target hhviterbialgorithm_with_celloff_and_ss -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h -[ 44%] Linking CXX executable a3m_extract -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -[ 45%] Linking CXX static library libCS_OBJECTS.a -[ 46%] Linking CXX executable a3m_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 44%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 -[ 46%] Built target a3m_extract /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o +/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp +/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 47%] Linking CXX executable a3m_database_reduce -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 -[ 48%] Linking CXX executable a3m_database_filter -[ 48%] Built target CS_OBJECTS -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -[ 48%] Built target a3m_reduce make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 48%] Built target a3m_database_reduce -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 49%] Linking CXX executable a3m_database_extract -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 -[ 49%] Built target a3m_database_filter +[ 44%] Built target CS_OBJECTS +[ 44%] Built target hhviterbialgorithm_with_celloff_and_ss cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h -[ 49%] Built target a3m_database_extract make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 49%] Built target generated +[ 44%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build +[ 46%] Linking CXX executable a3m_reduce +[ 45%] Linking CXX executable a3m_extract make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 +[ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o +[ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp +[ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp -[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp -[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp -[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 53%] Built target a3m_extract +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 54%] Linking CXX executable a3m_database_extract +[ 55%] Linking CXX executable a3m_database_reduce +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 +[ 55%] Built target a3m_reduce +[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 57%] Built target a3m_database_extract +[ 57%] Built target a3m_database_reduce +[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp +[ 60%] Linking CXX executable a3m_database_filter +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 60%] Built target a3m_database_filter [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o @@ -1140,11 +1176,22 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp +[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp +[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp +[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp +[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp +[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ -[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1166,17 +1213,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o 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-Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp -[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp -[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 @@ -1185,95 +1221,98 @@ make[4]: Leaving 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/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake "--color=" 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hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] @@ -1301,11 +1340,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 91%] Built target hhblits -[ 92%] Linking CXX executable hhblits_ca3m -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1333,14 +1367,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhalign -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 93%] Linking CXX executable hhsearch +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 93%] Built target hhalign +[ 94%] Linking CXX executable hhsearch_omp +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 94%] Built target hhblits /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ -[ 94%] Linking CXX executable hhalign_omp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1364,8 +1404,30 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 95%] Linking CXX executable hhblits_ca3m +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 95%] Built target hhsearch +[ 96%] Linking CXX executable hhblits_omp +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 96%] Built target hhsearch_omp +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 96%] Built target hhblits_ca3m +[ 97%] Linking CXX executable hhmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 97%] Built target hhblits_omp +[ 98%] Linking CXX executable hhconsensus +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 98%] Built target hhmake +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 98%] Built target hhconsensus /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1393,42 +1455,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 95%] Linking CXX executable hhsearch -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -[ 95%] Built target hhblits_ca3m -[ 96%] Linking CXX executable hhmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable hhblits_omp -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -[ 98%] Linking CXX executable hhsearch_omp -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 98%] Built target hhalign_omp -[ 99%] Linking CXX executable hhfilter -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' +[ 99%] Linking CXX executable hhalign_omp +cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[100%] Linking CXX executable hhfilter cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[100%] Linking CXX executable hhconsensus -cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 -[100%] Built target hhalign -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[100%] Built target hhmake -[100%] Built target hhsearch -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhfilter make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[100%] Built target hhsearch_omp -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[100%] Built target hhconsensus -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[100%] Built target hhblits_omp +[100%] Built target hhalign_omp [100%] Linking CXX executable cstranslate cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -1463,179 +1499,179 @@ debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh -- 03:33:49.844 INFO: query.a3m is in A2M, A3M or FASTA format +- 03:36:49.960 INFO: query.a3m is in A2M, A3M or FASTA format -- 03:33:50.321 INFO: Alternative alignment: 0 +- 03:36:50.348 INFO: Alternative alignment: 0 -- 03:33:50.335 INFO: 1 alignments done +- 03:36:50.356 INFO: 1 alignments done -- 03:33:50.368 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm +- 03:36:50.375 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 -Date Fri Sep 27 03:33:50 2024 +Date Fri Sep 27 03:36:50 2024 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) -query.a3m 0 32127 322 0 -query.a3m 0 32666 18 0 -query.a3m 0 32666 171 0 +query.a3m 0 32127 286 0 +query.a3m 0 32666 5 0 +query.a3m 0 32666 100 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... -- 03:33:52.084 INFO: Searching 1 column state sequences. +- 03:36:51.570 INFO: Searching 1 column state sequences. -- 03:33:52.184 INFO: query.a3m is in A2M, A3M or FASTA format +- 03:36:51.633 INFO: query.a3m is in A2M, A3M or FASTA format -- 03:33:52.202 INFO: Iteration 1 +- 03:36:51.649 INFO: Iteration 1 -- 03:33:52.765 INFO: Prefiltering database +- 03:36:52.050 INFO: Prefiltering database -- 03:33:53.292 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 03:36:52.332 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 03:33:53.300 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 03:36:52.333 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 03:33:53.301 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 03:36:52.333 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 03:33:53.301 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 03:36:52.333 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 03:33:53.370 INFO: Alternative alignment: 0 +- 03:36:52.373 INFO: Alternative alignment: 0 -- 03:33:53.384 INFO: 1 alignments done +- 03:36:52.379 INFO: 1 alignments done -- 03:33:53.385 INFO: Alternative alignment: 1 +- 03:36:52.379 INFO: Alternative alignment: 1 -- 03:33:53.396 INFO: 1 alignments done +- 03:36:52.386 INFO: 1 alignments done -- 03:33:53.397 INFO: Alternative alignment: 2 +- 03:36:52.386 INFO: Alternative alignment: 2 -- 03:33:53.397 INFO: Alternative alignment: 3 +- 03:36:52.386 INFO: Alternative alignment: 3 -- 03:33:54.041 INFO: Premerge done +- 03:36:52.757 INFO: Premerge done -- 03:33:54.042 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 03:36:52.758 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 03:33:54.071 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 03:36:52.785 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.27431 Searched_HMMs 1 -Date Fri Sep 27 03:33:54 2024 +Date Fri Sep 27 03:36:52 2024 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) -- 03:33:54.098 INFO: Searching 1 column state sequences. +- 03:36:52.808 INFO: Searching 1 column state sequences. -- 03:33:54.210 INFO: Thread 0 query.a3m +- 03:36:52.867 INFO: Thread 0 query.a3m -- 03:33:54.221 INFO: query.a3m is in A2M, A3M or FASTA format +- 03:36:52.878 INFO: query.a3m is in A2M, A3M or FASTA format -- 03:33:54.238 INFO: Iteration 1 +- 03:36:52.895 INFO: Iteration 1 -- 03:33:54.949 INFO: Prefiltering database +- 03:36:53.426 INFO: Prefiltering database -- 03:33:56.082 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 03:36:53.951 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 03:33:56.088 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 03:36:53.951 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 03:33:56.089 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 03:36:53.951 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 03:33:56.089 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 03:36:53.951 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 03:33:56.127 INFO: Alternative alignment: 0 +- 03:36:53.970 INFO: Alternative alignment: 0 -- 03:33:56.139 INFO: 1 alignments done +- 03:36:53.977 INFO: 1 alignments done -- 03:33:56.144 INFO: Alternative alignment: 1 +- 03:36:53.977 INFO: Alternative alignment: 1 -- 03:33:56.155 INFO: 1 alignments done +- 03:36:53.984 INFO: 1 alignments done -- 03:33:56.156 INFO: Alternative alignment: 2 +- 03:36:53.984 INFO: Alternative alignment: 2 -- 03:33:56.160 INFO: Alternative alignment: 3 +- 03:36:53.984 INFO: Alternative alignment: 3 -- 03:33:56.898 INFO: Premerge done +- 03:36:54.545 INFO: Premerge done -- 03:33:56.900 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 03:36:54.545 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 03:33:56.930 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 03:36:54.565 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 -- 03:33:57.103 INFO: query.a3m is in A2M, A3M or FASTA format +- 03:36:54.653 INFO: query.a3m is in A2M, A3M or FASTA format -- 03:33:57.132 INFO: Searching 1 database HHMs without prefiltering +- 03:36:54.669 INFO: Searching 1 database HHMs without prefiltering -- 03:33:57.133 INFO: Iteration 1 +- 03:36:54.669 INFO: Iteration 1 -- 03:33:57.629 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 03:36:54.990 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 03:33:57.698 INFO: Alternative alignment: 0 +- 03:36:55.028 INFO: Alternative alignment: 0 -- 03:33:57.711 INFO: 1 alignments done +- 03:36:55.035 INFO: 1 alignments done -- 03:33:57.711 INFO: Alternative alignment: 1 +- 03:36:55.035 INFO: Alternative alignment: 1 -- 03:33:57.720 INFO: 1 alignments done +- 03:36:55.042 INFO: 1 alignments done -- 03:33:57.720 INFO: Alternative alignment: 2 +- 03:36:55.042 INFO: Alternative alignment: 2 -- 03:33:57.720 INFO: Alternative alignment: 3 +- 03:36:55.042 INFO: Alternative alignment: 3 -- 03:33:58.187 INFO: Premerge done +- 03:36:55.411 INFO: Premerge done -- 03:33:58.187 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 03:36:55.411 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 03:33:58.217 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 03:36:55.441 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 -Date Fri Sep 27 03:33:58 2024 +Date Fri Sep 27 03:36:55 2024 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) -- 03:33:58.336 INFO: Thread 0 query.a3m +- 03:36:55.524 INFO: Thread 0 query.a3m -- 03:33:58.355 INFO: query.a3m is in A2M, A3M or FASTA format +- 03:36:55.536 INFO: query.a3m is in A2M, A3M or FASTA format -- 03:33:58.382 INFO: Searching 1 database HHMs without prefiltering +- 03:36:55.552 INFO: Searching 1 database HHMs without prefiltering -- 03:33:58.383 INFO: Iteration 1 +- 03:36:55.552 INFO: Iteration 1 -- 03:33:59.487 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 03:36:56.079 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 03:33:59.524 INFO: Alternative alignment: 0 +- 03:36:56.098 INFO: Alternative alignment: 0 -- 03:33:59.535 INFO: 1 alignments done +- 03:36:56.105 INFO: 1 alignments done -- 03:33:59.540 INFO: Alternative alignment: 1 +- 03:36:56.105 INFO: Alternative alignment: 1 -- 03:33:59.547 INFO: 1 alignments done +- 03:36:56.111 INFO: 1 alignments done -- 03:33:59.548 INFO: Alternative alignment: 2 +- 03:36:56.111 INFO: Alternative alignment: 2 -- 03:33:59.548 INFO: Alternative alignment: 3 +- 03:36:56.111 INFO: Alternative alignment: 3 -- 03:34:00.602 INFO: Premerge done +- 03:36:56.674 INFO: Premerge done -- 03:34:00.608 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 03:36:56.674 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 03:34:00.644 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 03:36:56.697 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp @@ -1777,9 +1813,9 @@ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb +dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. -dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1787,12 +1823,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1173700/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1173700/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/3287051 and its subdirectories -I: Current time: Thu Sep 26 15:35:09 -12 2024 -I: pbuilder-time-stamp: 1727408109 +I: removing directory /srv/workspace/pbuilder/1173700 and its subdirectories +I: Current time: Fri Sep 27 17:37:51 +14 2024 +I: pbuilder-time-stamp: 1727408271 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hhsuite_3.3.0+ds-8.diff: 93.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hhsuite_3.3.0+ds-8.diff.gz b2/build.log: 90.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 90.5% -- replaced with stdout Fri Sep 27 03:37:56 UTC 2024 I: diffoscope 277 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_hhsuite_unstable_arm64_1727408276 + touch /var/log/reproducible-builds/diffoscope_stamp_hhsuite_unstable_arm64_1727408276 + RESULT=0 + systemd-run '--description=diffoscope on hhsuite/3.3.0+ds-8 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_20-38708 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ --run-session -c jenkins-reproducible-unstable-diffoscope-62aa7047-1cb8-4978-a431-ad8f2f2a5f9e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/dbd-tmp-XWumuOI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1/hhsuite_3.3.0+ds-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2/hhsuite_3.3.0+ds-8_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_20-38708.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/hhsuite_3.3.0+ds-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b1/hhsuite_3.3.0+ds-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tpeY5JWQ/b2/hhsuite_3.3.0+ds-8_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.744s) 0.744s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.377s) 0.377s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.075s CPU time consumed: 1.073s _ _ _ _ | |__ | |__ ___ _ _(_) |_ ___ | '_ \| '_ \/ __| | | | | __/ _ \ | | | | | | \__ \ |_| | | || __/ |_| |_|_| |_|___/\__,_|_|\__\___| Fri Sep 27 03:37:57 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 27 03:37:57 UTC 2024 I: hhsuite from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-27 03:37:58] INFO: Starting at 2024-09-27 03:37:58.395598 [2024-09-27 03:37:58] INFO: Generating the pages of 1 package(s) [2024-09-27 03:37:58] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/hhsuite didn't produce a buildlog, even though it has been built. [2024-09-27 03:37:59] INFO: Finished at 2024-09-27 03:37:59.254863, took: 0:00:00.859272 Fri Sep 27 03:37:59 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/hhsuite.html Fri Sep 27 03:37:59 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Sep 27 03:37:59 UTC 2024 I: Submitting 12K b1/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc https://buildinfo.debian.net/60890a891a40d2180940cb244c8b0cf8b0fd4ebf/hhsuite_3.3.0+ds-8_all Fri Sep 27 03:38:00 UTC 2024 I: Submitting 12K b2/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc https://buildinfo.debian.net/cd8c2bf63bc60568b5ed99584cc4681b791875dd/hhsuite_3.3.0+ds-8_all Fri Sep 27 03:38:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Sep 27 03:38:01 UTC 2024 I: Done submitting .buildinfo files. Fri Sep 27 03:38:01 UTC 2024 I: Removing signed hhsuite_3.3.0+ds-8_arm64.buildinfo.asc files: removed './b1/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc' removed './b2/hhsuite_3.3.0+ds-8_arm64.buildinfo.asc' 1727408281 arm64 unstable hhsuite Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hhsuite_3.3.0+ds-8.rbuild.log: 89.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hhsuite_3.3.0+ds-8.rbuild.log.gz [2024-09-27 03:38:01] INFO: Starting at 2024-09-27 03:38:01.605266 [2024-09-27 03:38:01] INFO: Generating the pages of 1 package(s) [2024-09-27 03:38:02] INFO: Finished at 2024-09-27 03:38:02.152177, took: 0:00:00.546919 All cleanup done. Fri Sep 27 03:38:02 UTC 2024 - total duration: 0h 6m 50s. Fri Sep 27 03:38:02 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Au82Iu1u, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 54.410s CPU time consumed: 9.589s