I: pbuilder: network access will be disabled during build I: Current time: Wed May 15 07:56:58 +14 2024 I: pbuilder-time-stamp: 1715709418 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hhsuite_3.3.0+ds-7.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-7.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 26 03:36:26 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-7.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-7.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='9255' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WYgoK1Vc/pbuilderrc_Lb4f --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WYgoK1Vc/b2 --logfile b2/build.log --extrapackages usrmerge hhsuite_3.3.0+ds-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 06:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9255/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 ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libaom3{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcurl4{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libnghttp2-14{a} libnuma1{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx265-199{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl ghostscript gsfonts libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libsasl2-modules lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 43.0 MB of archives. After unpacking 171 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 liblocale-gettext-perl arm64 1.07-5 [15.1 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libfftw3-double3 arm64 3.3.10-1 [326 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libaom3 arm64 3.6.0-1 [1379 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libdav1d6 arm64 1.0.0-2 [274 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libde265-0 arm64 1.0.11-1 [148 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libx265-199 arm64 3.5-2+b1 [603 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 libheif1 arm64 1.15.1-1 [191 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-1 [1311 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 liblqr-1-0 arm64 0.4.2-2.1 [23.9 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libltdl7 arm64 2.4.7-5 [392 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-1+b1 [176 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.1 [99.1 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.1 [109 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [165 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libmagickcore-6.q16-6 arm64 8:6.9.11.60+dfsg-1.6 [1585 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libmagickwand-6.q16-6 arm64 8:6.9.11.60+dfsg-1.6 [348 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-7 [361 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 help2man arm64 1.49.3 [198 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 imagemagick-6.q16 arm64 8:6.9.11.60+dfsg-1.6 [339 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 imagemagick arm64 8:6.9.11.60+dfsg-1.6 [122 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Fetched 43.0 MB in 1s (43.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../01-libfftw3-double3_3.3.10-1_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../02-libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../03-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../04-libpng16-16_1.6.39-2_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../05-libfreetype6_2.12.1+dfsg-4_arm64.deb ... Unpacking libfreetype6:arm64 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../06-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../07-fontconfig-config_2.14.1-4_arm64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../08-libfontconfig1_2.14.1-4_arm64.deb ... Unpacking libfontconfig1:arm64 (2.14.1-4) ... Selecting previously unselected package libaom3:arm64. Preparing to unpack .../09-libaom3_3.6.0-1_arm64.deb ... Unpacking libaom3:arm64 (3.6.0-1) ... Selecting previously unselected package libdav1d6:arm64. Preparing to unpack .../10-libdav1d6_1.0.0-2_arm64.deb ... Unpacking libdav1d6:arm64 (1.0.0-2) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../11-libde265-0_1.0.11-1_arm64.deb ... Unpacking libde265-0:arm64 (1.0.11-1) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../12-libnuma1_2.0.16-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.16-1) ... Selecting previously unselected package libx265-199:arm64. Preparing to unpack .../13-libx265-199_3.5-2+b1_arm64.deb ... Unpacking libx265-199:arm64 (3.5-2+b1) ... Selecting previously unselected package libheif1:arm64. Preparing to unpack .../14-libheif1_1.15.1-1_arm64.deb ... Unpacking libheif1:arm64 (1.15.1-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../15-libjbig0_2.1-6.1_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../16-libjpeg62-turbo_1%3a2.1.5-2_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-2) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../17-liblcms2-2_2.14-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../18-libglib2.0-0_2.74.6-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.74.6-1) ... Selecting previously unselected package liblqr-1-0:arm64. Preparing to unpack .../19-liblqr-1-0_0.4.2-2.1_arm64.deb ... Unpacking liblqr-1-0:arm64 (0.4.2-2.1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../20-libltdl7_2.4.7-5_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-5) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../21-libopenjp2-7_2.5.0-1+b1_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.0-1+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../22-libdeflate0_1.14-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.14-1) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../23-liblerc4_4.0.0+ds-2_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-2) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../24-libwebp7_1.2.4-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../25-libtiff6_4.5.0-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.0-5) ... 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Preparing to unpack .../86-imagemagick-6.q16_8%3a6.9.11.60+dfsg-1.6_arm64.deb ... Unpacking imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package imagemagick. Preparing to unpack .../87-imagemagick_8%3a6.9.11.60+dfsg-1.6_arm64.deb ... Unpacking imagemagick (8:6.9.11.60+dfsg-1.6) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../88-libsimde-dev_0.7.4~rc2-2_all.deb ... Unpacking libsimde-dev (0.7.4~rc2-2) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libsimde-dev (0.7.4~rc2-2) ... Setting up liblcms2-2:arm64 (2.14-2) ... Setting up libaom3:arm64 (3.6.0-1) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up imagemagick-6-common (8:6.9.11.60+dfsg-1.6) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up liblerc4:arm64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.74.6-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:arm64 (1.44.2-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libdav1d6:arm64 (1.0.0-2) ... Setting up libltdl7:arm64 (2.4.7-5) ... Setting up libfftw3-double3:arm64 (3.3.10-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.1) ... Setting up libnuma1:arm64 (2.0.16-1) ... Setting up liblqr-1-0:arm64 (0.4.2-2.1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libtiff6:arm64 (4.5.0-5) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libopenjp2-7:arm64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libde265-0:arm64 (1.0.11-1) ... Setting up libwebpmux3:arm64 (1.2.4-0.1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:arm64 (3.6.2-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:arm64 (1.2.4-0.1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up libx265-199:arm64 (3.5-2+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:arm64 (7.88.1-7) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libheif1:arm64 (1.15.1-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libmagickcore-6.q16-6:arm64 (8:6.9.11.60+dfsg-1.6) ... Setting up cmake (3.25.1-1) ... Setting up libmagickwand-6.q16-6:arm64 (8:6.9.11.60+dfsg-1.6) ... Setting up debhelper (13.11.4) ... Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up imagemagick (8:6.9.11.60+dfsg-1.6) ... Processing triggers for libc-bin (2.36-8) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/9255/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/9255/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution I: Running cd /build/hhsuite-3.3.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hhsuite_3.3.0+ds-7_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss 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/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/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/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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 .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done 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CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && 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 .. -- Compiler is GNU -- Could NOT find MPI_C (missing: 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directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP 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-I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/as.cc [ 9%] Linking C static library libffindex.a cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/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/hhsuite-3.3.0+ds/mybuild' [ 9%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 10%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/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 [ 11%] Linking C executable ffindex_apply cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 11%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 12%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 15%] Linking C executable ffindex_reduce cd /build/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 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 15%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 16%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 17%] Linking C executable ffindex_build cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 17%] Built target ffindex_build 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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 19%] Linking C executable ffindex_from_fasta cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 19%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 21%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /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/hhsuite-3.3.0+ds/mybuild' [ 22%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp [ 24%] Linking C executable ffindex_get cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 24%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 26%] Linking C executable ffindex_modify cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 [ 27%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a [ 28%] Generating ../generated/context_data.lib.h cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /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/hhsuite-3.3.0+ds/mybuild' [ 28%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= [ 28%] Built target hhviterbialgorithm_with_celloff 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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 31%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 32%] Linking C executable ffindex_unpack cd /build/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%] Built target hhviterbialgorithm_with_celloff_and_ss /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --color= [ 33%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 [ 34%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_extract.cpp /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 34%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --color= [ 34%] Built target hhviterbialgorithm_and_ss make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 35%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 36%] Linking C executable ffindex_order cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 37%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a [ 38%] Linking C executable ffindex_from_fasta_with_split cd /build/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 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 38%] Built target ffindex_order make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 38%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color= [ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 40%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 41%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/log.cc [ 42%] Linking CXX executable a3m_extract cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 42%] Built target a3m_extract [ 43%] Linking CXX executable a3m_reduce cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 [ 44%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/application.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 45%] Linking CXX executable a3m_database_reduce cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 45%] Built target a3m_reduce [ 46%] Generating ../generated/cs219.lib.h cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 46%] Built target a3m_database_reduce [ 47%] Linking CXX executable a3m_database_extract cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 47%] Built target a3m_database_extract make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 47%] Built target generated [ 48%] Linking CXX executable a3m_database_filter cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 48%] Built target a3m_database_filter [ 49%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/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/hhsuite-3.3.0+ds/mybuild' [ 49%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/hhsuite-3.3.0+ds/mybuild' [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhblits.cpp [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhalign.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhsearch.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp /build/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/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/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/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 ()); | ~~~~~~~~~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP 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CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 88%] Linking CXX executable hhalign cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 89%] Linking CXX executable hhsearch cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 90%] Linking CXX executable hhblits cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 90%] Built target hhalign make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 91%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 91%] Built target hhsearch make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend [ 91%] Built target hhblits make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 92%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 93%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 [ 95%] Linking CXX executable hhfilter cd /build/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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 95%] Built target hhfilter [ 96%] Linking CXX executable hhmake cd /build/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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 96%] Built target hhblits_omp [ 97%] Linking CXX executable hhconsensus cd /build/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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 97%] Built target hhmake make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 97%] Built target hhconsensus /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/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/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhblits_ca3m cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 [ 99%] Linking CXX executable hhalign_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [100%] Linking CXX executable hhsearch_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_ca3m make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhalign_omp make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhsearch_omp [100%] Linking CXX executable cstranslate cd /build/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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/data /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Nothing to be done for 'data/CMakeFiles/generated.dir/build'. make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/hhsuite-3.3.0+ds' cd /build/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-3.3.0+ds/mybuild/src:/build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh - 08:02:28.930 INFO: query.a3m is in A2M, A3M or FASTA format - 08:02:30.997 INFO: Alternative alignment: 0 - 08:02:31.049 INFO: 1 alignments done - 08:02:31.192 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 Wed May 15 08:02:31 2024 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) query.a3m 0 32127 1027 0 query.a3m 0 32666 7 0 query.a3m 0 32666 267 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 08:02:36.672 INFO: Searching 1 column state sequences. - 08:02:36.853 INFO: query.a3m is in A2M, A3M or FASTA format - 08:02:36.923 INFO: Iteration 1 - 08:02:38.274 INFO: Prefiltering database - 08:02:39.605 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 08:02:39.605 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 08:02:39.605 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 08:02:39.605 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 08:02:39.799 INFO: Alternative alignment: 0 - 08:02:39.848 INFO: 1 alignments done - 08:02:39.848 INFO: Alternative alignment: 1 - 08:02:39.891 INFO: 1 alignments done - 08:02:39.891 INFO: Alternative alignment: 2 - 08:02:39.891 INFO: Alternative alignment: 3 - 08:02:41.513 INFO: Premerge done - 08:02:41.513 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 08:02:41.664 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 Wed May 15 08:02:41 2024 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) - 08:02:41.773 INFO: Searching 1 column state sequences. - 08:02:42.110 INFO: Thread 0 query.a3m - 08:02:42.175 INFO: query.a3m is in A2M, A3M or FASTA format - 08:02:42.248 INFO: Iteration 1 - 08:02:45.387 INFO: Prefiltering database - 08:02:48.537 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 08:02:48.537 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 08:02:48.537 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 08:02:48.537 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 08:02:48.631 INFO: Alternative alignment: 0 - 08:02:48.666 INFO: 1 alignments done - 08:02:48.666 INFO: Alternative alignment: 1 - 08:02:48.703 INFO: 1 alignments done - 08:02:48.703 INFO: Alternative alignment: 2 - 08:02:48.703 INFO: Alternative alignment: 3 - 08:02:52.046 INFO: Premerge done - 08:02:52.046 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 08:02:52.151 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 08:02:52.426 INFO: query.a3m is in A2M, A3M or FASTA format - 08:02:52.495 INFO: Searching 1 database HHMs without prefiltering - 08:02:52.495 INFO: Iteration 1 - 08:02:53.794 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 08:02:53.995 INFO: Alternative alignment: 0 - 08:02:54.042 INFO: 1 alignments done - 08:02:54.042 INFO: Alternative alignment: 1 - 08:02:54.077 INFO: 1 alignments done - 08:02:54.077 INFO: Alternative alignment: 2 - 08:02:54.077 INFO: Alternative alignment: 3 - 08:02:55.691 INFO: Premerge done - 08:02:55.691 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 08:02:55.839 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 Wed May 15 08:02:55 2024 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) - 08:02:56.271 INFO: Thread 0 query.a3m - 08:02:56.336 INFO: query.a3m is in A2M, A3M or FASTA format - 08:02:56.407 INFO: Searching 1 database HHMs without prefiltering - 08:02:56.407 INFO: Iteration 1 - 08:02:59.139 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 08:02:59.239 INFO: Alternative alignment: 0 - 08:02:59.286 INFO: 1 alignments done - 08:02:59.286 INFO: Alternative alignment: 1 - 08:02:59.340 INFO: 1 alignments done - 08:02:59.340 INFO: Alternative alignment: 2 - 08:02:59.340 INFO: Alternative alignment: 3 - 08:03:02.249 INFO: Premerge done - 08:03:02.250 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 08:03:02.352 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/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/hhsuite-3.3.0+ds' mkdir -p /build/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild cd mybuild && make -j8 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/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/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j8 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/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/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/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-7_arm64.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-7_arm64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-7_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-7_arm64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/9255/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/9255/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/9255 and its subdirectories I: Current time: Wed May 15 08:05:15 +14 2024 I: pbuilder-time-stamp: 1715709915