Tue Oct 21 16:45:24 UTC 2025 I: starting to build hhsuite/forky/arm64 on jenkins on '2025-10-21 16:45' Tue Oct 21 16:45:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/101693/console.log Tue Oct 21 16:45:24 UTC 2025 I: Downloading source for forky/hhsuite=3.3.0+ds-9 --2025-10-21 16:45:24-- http://deb.debian.org/debian/pool/main/h/hhsuite/hhsuite_3.3.0%2bds-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2153 (2.1K) [text/prs.lines.tag] Saving to: ‘hhsuite_3.3.0+ds-9.dsc’ 0K .. 100% 245M=0s 2025-10-21 16:45:24 (245 MB/s) - ‘hhsuite_3.3.0+ds-9.dsc’ saved [2153/2153] Tue Oct 21 16:45:24 UTC 2025 I: hhsuite_3.3.0+ds-9.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-9 Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille , Sascha Steinbiss , Homepage: https://toolkit.tuebingen.mpg.de/ Standards-Version: 4.7.2 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 128e4d8b43032a85c68321b4a4661e17c1f23044 16904 hhsuite_3.3.0+ds-9.debian.tar.xz Checksums-Sha256: a81037f2e2a4801f1a42f5aa5939334fe038053d05ceabdc0899fefb8cc00a44 4775072 hhsuite_3.3.0+ds.orig.tar.xz 930c7195042d4c83975b99039a4df4904041a557a8d142f38dcc94f4ecc3f900 16904 hhsuite_3.3.0+ds-9.debian.tar.xz Files: d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz 4bb89a0a1a1f74616d3a20353441f119 16904 hhsuite_3.3.0+ds-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmjyZMkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGUng/8DARYxNCdXH2u7niHsiA+3O/aP9vlylHN nHOhDi1BU+CDGNYwKls9rRqbY2vsPqe/JagvsbBqLDOqY62TC0j7/pY+5MK8ZdcB PumSfXSbbaA4FsOOxjlInYXa1HrXO9n+NtfAXuFQ9GGZmxRtVEytKcVZ3XDF5lA7 6YpsPCuBR9cMclyE0bfLEwM5ALZJKi4w4KSB90oRQOOPfti1TQSc3GKz+ydAqxdc MmC+Uhe2mF/TYidVBRtm8bd2FBEVgYuhIr/at5kwgb7UOrdempVKG3ewvTmkdCWW JtIc/XkO1bHDmY2DSv2gN+7EHGsWwdquQu3m/Lc1sMKv6/qaFULSZm2Ja4NtWD6y iMtJgD/Js467eN6uDOBCNasJg+3fSHRNtkWXcYa1WEKm4UYHYhBYC1jKGKjwR5wG KcT/sTWAWPZTB9Q3fa7xbCz57w5V1z7PhjdqXIHsYqn119zh0bR/KmRJpQiRbQFK C4zPbBH20wqD5T+/wOVUYooYDU1YHiKBXTiK3VXJz/qPLHP+XyIUwam1mR+s+pPf Bs4RMJ4g8YIZSyxWtBRCkwLPAdn9sxBfqVUufE/7o7be8q/R1vWKZT13nIHtV4AS /q4P0CJZbSVihhlvKrFnZi2xhkwmzws3uVViq3DSnsdXKMwyhLvFEIQ2k0hetwJu TpJWe3iaTro= =Uxj1 -----END PGP SIGNATURE----- Tue Oct 21 16:45:24 UTC 2025 I: Checking whether the package is not for us Tue Oct 21 16:45:24 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Oct 21 16:45:24 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Oct 21 16:50:55 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 23 11:08:31 -12 2026 I: pbuilder-time-stamp: 1795475311 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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-9.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-9.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-9.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-9.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/1263277/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='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='171ec9fe9a394ae4b141a5b63eb36d89' 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='1263277' 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.G1BKMqR7/pbuilderrc_TscF --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/b1 --logfile b1/build.log hhsuite_3.3.0+ds-9.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' 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 codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1263277/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 ... 20000 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-7-common{a} imagemagick-7.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} libffi8{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgnutls30t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libidn2-0{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-7.q16-10{a} libmagickwand-7.q16-10{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-ossl0{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libraw23t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsimde-dev{a} libssh2-1t64{a} libtasn1-6{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{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-7.q16-10-extra libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 41.9 MB of archives. After unpacking 165 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libheif-plugin-dav1d arm64 1.20.2-2+b1 [18.1 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 libde265-0 arm64 1.0.16-1 [153 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 libheif-plugin-libde265 arm64 1.20.2-2+b1 [16.9 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libheif1 arm64 1.20.2-2+b1 [504 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libglib2.0-0t64 arm64 2.86.0-5 [1434 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b2 [27.0 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libltdl7 arm64 2.5.4-5 [415 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libraw23t64 arm64 0.21.4-2 [371 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 imagemagick-7-common all 8:7.1.2.3+dfsg1-1 [69.0 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libmagickcore-7.q16-10 arm64 8:7.1.2.3+dfsg1-1 [1660 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libmagickwand-7.q16-10 arm64 8:7.1.2.3+dfsg1-1 [270 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 67 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-2 [1395 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-4 [368 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 87 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 93 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 imagemagick-7.q16 arm64 8:7.1.2.3+dfsg1-1 [728 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 imagemagick arm64 8:7.1.2.3+dfsg1-1 [21.6 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 41.9 MB in 0s (144 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20000 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../001-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... 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Setting up imagemagick-7.q16 (8:7.1.2.3+dfsg1-1) ... update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist Setting up imagemagick (8:7.1.2.3+dfsg1-1) ... Processing triggers for libc-bin (2.41-12) ... 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-9_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- 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 (2.6s) -- 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 CMAKE_POLICY_VERSION_MINIMUM 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- 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 (0.6s) -- 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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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[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/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.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/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" 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 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/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' 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 -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[4]: Leaving 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/build make[4]: Entering 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' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.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' [ 2%] Generating ../generated/context_data.crf.h make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build 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 [ 3%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated 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 -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 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 [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o make[4]: Leaving 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 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 make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.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 [ 6%] Generating ../generated/cs219.lib.h make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' 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/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%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o 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 [ 8%] Generating ../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/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 [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o [ 10%] 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/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/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.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/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/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/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 && /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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 14%] Built target ffindex [ 15%] 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 /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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, 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++/15/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.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_apply.dir/DependInfo.cmake "--color=" 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 -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' [ 17%] 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 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=" 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%] 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 [ 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 /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 -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 19%] 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 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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_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 -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 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-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 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 -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d 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%] Built target ffindex_reduce 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' make -f 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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 [ 25%] Linking C executable ffindex_build [ 25%] 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 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 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_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%] 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 /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 -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a 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 -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d 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' [ 26%] Built target ffindex_from_fasta 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=" [ 26%] Built target ffindex_build 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=" 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' 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' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o [ 28%] Linking C executable ffindex_get 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 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 [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.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_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 [ 30%] Linking C executable ffindex_modify 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/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 -Wl,--dependency-file=CMakeFiles/ffindex_get.dir/link.d CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 30%] 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 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=" 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]: 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 -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 31%] 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 [ 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 [ 32%] Built target ffindex_modify [ 33%] 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 -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 33%] Built target ffindex_unpack /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 -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 33%] Built target ffindex_order [ 34%] 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/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 -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d 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' [ 34%] Built target ffindex_from_fasta_with_split [ 35%] 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 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 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 [ 36%] Linking CXX static library libhhviterbialgorithm_and_ss.a /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' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake [ 36%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend 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_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_extract.dir/DependInfo.cmake "--color=" 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_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 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=" 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=" 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 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]: 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/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build 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/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 -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.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[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 make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.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/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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 38%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o [ 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 -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 && /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 [ 41%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o [ 41%] 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 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 [ 41%] Built target hhviterbialgorithm_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 [ 42%] 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 [ 43%] 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/hhviterbialgorithm_with_celloff.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' [ 43%] Built target hhviterbialgorithm_with_celloff_and_ss /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 43%] Built target hhviterbialgorithm_with_celloff [ 44%] Linking CXX static library libCS_OBJECTS.a 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/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/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Built target CS_OBJECTS [ 45%] Linking CXX executable a3m_reduce 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 [ 46%] 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 [ 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_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 /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 -Wl,--dependency-file=CMakeFiles/a3m_extract.dir/link.d CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.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 -Wl,--dependency-file=CMakeFiles/a3m_reduce.dir/link.d CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_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' [ 48%] Built target a3m_reduce [ 48%] Built target a3m_extract /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 -Wl,--dependency-file=CMakeFiles/a3m_database_reduce.dir/link.d 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' [ 48%] Built target a3m_database_reduce /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 -Wl,--dependency-file=CMakeFiles/a3m_database_extract.dir/link.d 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' [ 48%] Built target a3m_database_extract [ 49%] 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 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 -Wl,--dependency-file=CMakeFiles/a3m_database_filter.dir/link.d 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' [ 49%] Built target a3m_database_filter 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' [ 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' [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.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/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 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 [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.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 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 [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o [ 58%] 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 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 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 [ 59%] 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 -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/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/util.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.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/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 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 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/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.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/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 [ 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 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 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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/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 -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 [ 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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, 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 src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.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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-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 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/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 [ 90%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.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.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 [ 91%] 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 /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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, 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 ()); | ~~~~~~~~~~~~~~~~~ /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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, 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 ()); | ~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable hhblits_omp /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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, 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/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 -Wl,--dependency-file=CMakeFiles/hhsearch.dir/link.d 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' [ 92%] Built target hhsearch [ 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 /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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, 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 ()); | ~~~~~~~~~~~~~~~~~ [ 94%] 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 [ 95%] 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 [ 96%] 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 -Wl,--dependency-file=CMakeFiles/hhblits_omp.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 96%] Built target hhblits_omp /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 -Wl,--dependency-file=CMakeFiles/hhalign.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 96%] Built target hhalign [ 97%] 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 [ 98%] 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 -Wl,--dependency-file=CMakeFiles/hhblits_ca3m.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhblits_ca3m /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 -Wl,--dependency-file=CMakeFiles/hhalign_omp.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhalign_omp /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 -Wl,--dependency-file=CMakeFiles/hhblits.dir/link.d 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 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhblits /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 -Wl,--dependency-file=CMakeFiles/hhfilter.dir/link.d 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' [ 98%] Built target hhfilter /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 -Wl,--dependency-file=CMakeFiles/hhsearch_omp.dir/link.d 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 hhsearch_omp [ 99%] 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 -Wl,--dependency-file=CMakeFiles/hhmake.dir/link.d 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' [ 99%] Built target hhmake [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 /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 -Wl,--dependency-file=CMakeFiles/hhconsensus.dir/link.d 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 hhconsensus [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 -Wl,--dependency-file=CMakeFiles/cstranslate.dir/link.d 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 - 23:12:42.327 INFO: query.a3m is in A2M, A3M or FASTA format - 23:12:42.687 INFO: Alternative alignment: 0 - 23:12:42.694 INFO: 1 alignments done - 23:12:42.715 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 Mon Nov 23 23:12:42 2026 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 283 0 query.a3m 0 32666 3 0 query.a3m 0 32666 118 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 23:12:43.858 INFO: Searching 1 column state sequences. - 23:12:43.924 INFO: query.a3m is in A2M, A3M or FASTA format - 23:12:43.941 INFO: Iteration 1 - 23:12:44.275 INFO: Prefiltering database - 23:12:44.570 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:12:44.571 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:12:44.571 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:12:44.571 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:12:44.611 INFO: Alternative alignment: 0 - 23:12:44.617 INFO: 1 alignments done - 23:12:44.617 INFO: Alternative alignment: 1 - 23:12:44.624 INFO: 1 alignments done - 23:12:44.624 INFO: Alternative alignment: 2 - 23:12:44.624 INFO: Alternative alignment: 3 - 23:12:44.970 INFO: Premerge done - 23:12:44.970 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:12:44.999 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 Mon Nov 23 23:12:44 2026 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) - 23:12:45.022 INFO: Searching 1 column state sequences. - 23:12:45.079 INFO: Thread 0 query.a3m - 23:12:45.089 INFO: query.a3m is in A2M, A3M or FASTA format - 23:12:45.106 INFO: Iteration 1 - 23:12:45.665 INFO: Prefiltering database - 23:12:46.227 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:12:46.227 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:12:46.227 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:12:46.227 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:12:46.248 INFO: Alternative alignment: 0 - 23:12:46.255 INFO: 1 alignments done - 23:12:46.255 INFO: Alternative alignment: 1 - 23:12:46.262 INFO: 1 alignments done - 23:12:46.262 INFO: Alternative alignment: 2 - 23:12:46.262 INFO: Alternative alignment: 3 - 23:12:46.859 INFO: Premerge done - 23:12:46.859 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:12:46.880 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 23:12:46.971 INFO: query.a3m is in A2M, A3M or FASTA format - 23:12:46.988 INFO: Searching 1 database HHMs without prefiltering - 23:12:46.988 INFO: Iteration 1 - 23:12:47.280 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:12:47.321 INFO: Alternative alignment: 0 - 23:12:47.327 INFO: 1 alignments done - 23:12:47.327 INFO: Alternative alignment: 1 - 23:12:47.335 INFO: 1 alignments done - 23:12:47.335 INFO: Alternative alignment: 2 - 23:12:47.335 INFO: Alternative alignment: 3 - 23:12:47.711 INFO: Premerge done - 23:12:47.712 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:12:47.741 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 Mon Nov 23 23:12:47 2026 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) - 23:12:47.828 INFO: Thread 1 query.a3m - 23:12:47.842 INFO: query.a3m is in A2M, A3M or FASTA format - 23:12:47.859 INFO: Searching 1 database HHMs without prefiltering - 23:12:47.859 INFO: Iteration 1 - 23:12:48.425 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:12:48.450 INFO: Alternative alignment: 0 - 23:12:48.456 INFO: 1 alignments done - 23:12:48.456 INFO: Alternative alignment: 1 - 23:12:48.463 INFO: 1 alignments done - 23:12:48.463 INFO: Alternative alignment: 2 - 23:12:48.463 INFO: Alternative alignment: 3 - 23:12:49.060 INFO: Premerge done - 23:12:49.060 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:12:49.084 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 (= 0.8.2-3), " 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-9_arm64.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-9_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-9_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-9_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-9_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/1263277 and its subdirectories I: Current time: Mon Nov 23 11:13:35 -12 2026 I: pbuilder-time-stamp: 1795475615 Tue Oct 21 16:50:55 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Oct 21 16:50:55 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Oct 21 17:00:58 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Oct 21 17:00:59 UTC 2025 I: hhsuite_3.3.0+ds-9_arm64.changes: Format: 1.8 Date: Fri, 17 Oct 2025 17:36:29 +0200 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: all arm64 Version: 3.3.0+ds-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hhsuite - sensitive protein sequence searching based on HMM-HMM alignment hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment ( Closes: 1112991 Changes: hhsuite (3.3.0+ds-9) unstable; urgency=medium . * Fix build with CMake 4 Closes: #1112991 * d/watch: version=5 * Standards-Version: 4.7.2 (routine-update) * debputy lint --auto-fix (routine-update) Checksums-Sha1: d44daca7409b25e92eea6ff8f2dfbd70a745bf7b 4401984 hhsuite-data_3.3.0+ds-9_all.deb d1ca4c702abf51692f2c24c4b3a8cd4090e076ee 20481984 hhsuite-dbgsym_3.3.0+ds-9_arm64.deb dafe95a1d5f50d76eaa493ec6c41ed987499e4df 7485 hhsuite_3.3.0+ds-9_arm64.buildinfo bf22a6dd24afa357f45c48e3fbfbc1cce56b0f09 10436792 hhsuite_3.3.0+ds-9_arm64.deb Checksums-Sha256: 14e5361537874eb5582dcbc919ad35ea3467257d8fb2302f1849512e4fbe2fae 4401984 hhsuite-data_3.3.0+ds-9_all.deb 4d4f9fd3aba15537d1a4e5f41d6488012cca6da5e847cdb62cefc0cbc84d2f1d 20481984 hhsuite-dbgsym_3.3.0+ds-9_arm64.deb 72f7848a9dbbefb1589d3c915b26a514afcf5f745d45bd6e147fc6ca3cdb4947 7485 hhsuite_3.3.0+ds-9_arm64.buildinfo ee0b035c0e6c47bbdfbd44265dea2a9bd5776a60a524052fa01496d7bbbb61c6 10436792 hhsuite_3.3.0+ds-9_arm64.deb Files: 60efb3bba649f78b1163675976702217 4401984 science optional hhsuite-data_3.3.0+ds-9_all.deb a0f6b980b5ba38a431631979efc6cac7 20481984 debug optional hhsuite-dbgsym_3.3.0+ds-9_arm64.deb 93dd13749f1abe6e848399f523003691 7485 science optional hhsuite_3.3.0+ds-9_arm64.buildinfo b776e45914bdebdf00813f92caf9655a 10436792 science optional hhsuite_3.3.0+ds-9_arm64.deb Tue Oct 21 17:00:59 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_4-101693.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/hhsuite_3.3.0+ds-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/hhsuite_3.3.0+ds-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/hhsuite_3.3.0+ds-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/b1/hhsuite_3.3.0+ds-9_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.G1BKMqR7/b2/hhsuite_3.3.0+ds-9_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 210ms CPU time consumed: 168ms Memory peak: 17.8M (swap: 0B) Tue Oct 21 17:01:00 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 21 17:01:00 UTC 2025 I: hhsuite from forky built successfully and reproducibly on arm64. Tue Oct 21 17:01:01 UTC 2025 I: Removing signed hhsuite_3.3.0+ds-9_arm64.buildinfo.asc files: removed './b1/hhsuite_3.3.0+ds-9_arm64.buildinfo.asc' removed './b2/hhsuite_3.3.0+ds-9_arm64.buildinfo.asc'