I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 16:34:28 -12 2023 I: pbuilder-time-stamp: 1683261268 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 Tue Oct 25 01:36:26 2022 -12 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/9287/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='0a115c79d5fa4d3fa47ebaf043567ec3' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='9287' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.masyQHVx/pbuilderrc_QNFU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.masyQHVx/b1 --logfile b1/build.log hhsuite_3.3.0+ds-7.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux jtx1c 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/9287/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: armhf 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 ... 19329 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} 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, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 39.8 MB of archives. After unpacking 140 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libaom3 armhf 3.6.0-1 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libdav1d6 armhf 1.0.0-2 [256 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libde265-0 armhf 1.0.11-1 [143 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libx265-199 armhf 3.5-2+b1 [580 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libheif1 armhf 1.15.1-1 [183 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf liblcms2-2 armhf 2.14-2 [125 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libopenjp2-7 armhf 2.5.0-1+b1 [170 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.1 [242 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-5 [295 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libwebpdemux2 armhf 1.2.4-0.1 [98.2 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libwebpmux3 armhf 1.2.4-0.1 [105 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [165 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [1634 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [402 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 76 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 78 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.6 [338 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.6 [122 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libsimde-dev all 0.7.4~rc2-2 [377 kB] Fetched 39.8 MB in 12s (3379 kB/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 ... 19329 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libfftw3-double3:armhf. Preparing to unpack .../01-libfftw3-double3_3.3.10-1_armhf.deb ... Unpacking libfftw3-double3:armhf (3.3.10-1) ... Selecting previously unselected package libexpat1:armhf. 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Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (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:armhf (2.1-6.1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:armhf (1.44.2-1) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:armhf (2:4.0.2-3) ... Setting up libpng16-16:armhf (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:armhf (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libdav1d6:armhf (1.0.0-2) ... Setting up libltdl7:armhf (2.4.7-5) ... Setting up libfftw3-double3:armhf (3.3.10-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libx265-199:armhf (3.5-2+b1) ... Setting up libwebp7:armhf (1.2.4-0.1) ... Setting up liblqr-1-0:armhf (0.4.2-2.1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:armhf (1.4.3-3) ... Setting up libtiff6:armhf (4.5.0-5) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libopenjp2-7:armhf (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libde265-0:armhf (1.0.11-1) ... Setting up libwebpmux3:armhf (1.2.4-0.1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... 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:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:armhf (3.6.2-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:armhf (1.2.4-0.1) ... Setting up libheif1:armhf (1.15.1-1) ... Setting up libldap-2.5-0:armhf (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:armhf (2.12.1+dfsg-5) ... 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:armhf (7.88.1-9) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libfontconfig1:armhf (2.14.1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (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:armhf (8:6.9.11.60+dfsg-1.6) ... Setting up cmake (3.25.1-1) ... Setting up libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.6) ... Setting up debhelper (13.11.4) ... 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Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/hhsuite-3.3.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hhsuite_3.3.0+ds-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 armhf 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/arm-linux-gnueabihf -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 -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/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/arm-linux-gnueabihf -DNATIVE_ARCH=0 .. -- Compiler is GNU -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP -- Configuring done -- Generating done -- 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_build-arch make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild cd mybuild && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 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 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-3.3.0+ds/mybuild//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' 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= 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.dir/DependInfo.cmake --color= 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/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving 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.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 3%] Generating ../generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o [ 3%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o 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/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/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c 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_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp 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 /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c: In function 'ffindex_index_parse': /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c:291:43: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 291 | fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes); | ~~^ ~~~~~~ | | | | long int size_t {aka unsigned int} | %d [ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.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.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 5%] 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' [ 5%] Built target ffindex [ 6%] 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/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 [ 7%] 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 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 /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' [ 7%] Built target hhviterbialgorithm_with_celloff [ 8%] 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 && /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 -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/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/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 9%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.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 -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 cd /build/hhsuite-3.3.0+ds/data && /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 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 cd /build/hhsuite-3.3.0+ds/data && /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 make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.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/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.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 -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/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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 10%] Built target generated make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_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/cs /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src/cs /build/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.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/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/aa.cc [ 12%] 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 [ 13%] 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' [ 13%] Built target hhviterbialgorithm_with_celloff_and_ss [ 14%] 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 make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.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_COMPRESS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 14%] 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 [ 15%] 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 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 /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)) | ^~~~~~~ /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' [ 15%] Built target hhviterbialgorithm_and_ss [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o [ 17%] 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 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 [ 18%] 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 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' [ 18%] Built target A3M_COMPRESS [ 19%] 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 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' [ 20%] 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:172:42: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned 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 int size_t {aka unsigned int} | %d /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:47: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned 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 int size_t {aka unsigned int} | %d [ 21%] 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' [ 21%] Built target ffindex_apply [ 22%] 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 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' [ 23%] 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 [ 24%] 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' [ 24%] 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 -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_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.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.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o [ 26%] 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_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 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 [ 27%] 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 [ 28%] 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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /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 [ 28%] 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' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 29%] 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 [ 29%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/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' [ 30%] 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 [ 31%] 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' [ 32%] 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 [ 32%] 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= /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 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' [ 33%] 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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 33%] 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= 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' [ 34%] 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 [ 35%] 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 /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[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 35%] Built target ffindex_unpack 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= [ 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 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' /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 [ 37%] 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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 37%] Built target ffindex_order 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= 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' [ 38%] 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 [ 39%] 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' [ 39%] Built target ffindex_from_fasta_with_split 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= 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' [ 40%] 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 [ 41%] 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' [ 41%] Built target CS_OBJECTS 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_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 42%] 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 [ 43%] 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' [ 43%] Built target a3m_extract 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]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 44%] 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 [ 45%] 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 /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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 45%] Built target a3m_reduce 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= 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' [ 46%] 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 [ 47%] 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' [ 47%] Built target a3m_database_reduce 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' [ 48%] 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 [ 49%] 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 /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' [ 49%] Built target a3m_database_extract [ 50%] 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 [ 51%] 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' [ 51%] Built target a3m_database_filter [ 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/hhsearch.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/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 [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.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 [ 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/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 In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/hhhit.h:14, from /build/hhsuite-3.3.0+ds/src/hhhitlist.h:16, from /build/hhsuite-3.3.0+ds/src/hhhitlist.cpp:9: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator]', inlined from 'void HitList::PrintMatrices(HMM*, std::stringstream&, bool, size_t, const float (*)[20])' at /build/hhsuite-3.3.0+ds/src/hhhitlist.cpp:591:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 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 /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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 [ 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 In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/hhsuite-3.3.0+ds/lib/simd/simd.h:9, from /build/hhsuite-3.3.0+ds/src/util.h:23, from /build/hhsuite-3.3.0+ds/src/hhhmm.h:8, from /build/hhsuite-3.3.0+ds/src/hhprefilter.h:17, from /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:8: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ [ 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 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 [ 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 -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/hhprefilter.h:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:531:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1625 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/12/bits/stl_algo.h:1916:27: /usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1900 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'void Prefilter::prefilter_db(HMM*, Hash*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector > >&, std::vector > >&)' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'void Prefilter::prefilter_db(HMM*, Hash*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector > >&, std::vector > >&)' at /build/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.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/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.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/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfunc.cpp In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/util.h:20, from /build/hhsuite-3.3.0+ds/src/hhhmm.h:8, from /build/hhsuite-3.3.0+ds/src/hhhmmsimd.h:5, from /build/hhsuite-3.3.0+ds/src/hhviterbirunner.h:4, from /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:1: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator]', inlined from 'void ViterbiConsumerThread::align(int, int, float, char)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:67:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator]', inlined from 'void ViterbiRunner::merge_thread_results(std::vector&, std::vector&, std::map, std::vector >&, std::vector&, int, float)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:259:31, inlined from 'std::vector ViterbiRunner::alignment(Parameters&, HMMSimd*, std::vector, float, float*, const float (*)[20], const float (*)[20], const float (*)[20], int, const float (*)[4][11], const float (*)[11][4][11], const float (*)[11][8])' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:173:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator]', inlined from 'void ViterbiRunner::merge_thread_results(std::vector&, std::vector&, std::map, std::vector >&, std::vector&, int, float)' at /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:259:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make[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.dir/DependInfo.cmake --color= 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/hhmake.dir/DependInfo.cmake --color= 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 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src/CMakeFiles/hhmake.dir/hhmake.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/hhfilter.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfilter.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/hhblits.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_app.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/hhmake.dir/hhmake.cpp.o -MF CMakeFiles/hhmake.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhmake.cpp [ 83%] 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' [ 83%] Built target hhblits make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.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.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 84%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.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 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-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 [ 86%] 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' [ 86%] Built target hhfilter make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.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/hhalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 87%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.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 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'/build/hhsuite-3.3.0+ds/mybuild' [ 89%] Built target hhsearch make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.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/cstranslate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 90%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.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/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 [ 91%] 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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 91%] Built target hhalign make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_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/hhblits_omp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 92%] Building CXX object src/CMakeFiles/hhblits_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 -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 93%] 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' [ 93%] Built target hhconsensus 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' [ 94%] 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 /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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ [ 95%] 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 /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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 95%] Built target hhblits_omp make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_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/hhalign_omp.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]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 96%] 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 /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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ [ 97%] 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' [ 97%] Built target hhsearch_omp 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/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 98%] 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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 99%] Built target hhalign_omp /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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ [100%] 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 /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 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_ca3m [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 -j3 "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 - 16:39:31.622 INFO: query.a3m is in A2M, A3M or FASTA format - 16:39:33.180 INFO: Alternative alignment: 0 - 16:39:33.301 INFO: 1 alignments done - 16:39:33.464 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 Thu May 4 16:39:33 2023 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 1138 0 query.a3m 0 32666 11 0 query.a3m 0 32666 245 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 16:39:37.562 INFO: Searching 1 column state sequences. - 16:39:37.728 INFO: query.a3m is in A2M, A3M or FASTA format - 16:39:37.781 INFO: Iteration 1 - 16:39:39.101 INFO: Prefiltering database - 16:39:40.436 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 16:39:40.447 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 16:39:40.447 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 16:39:40.447 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 16:39:40.617 INFO: Alternative alignment: 0 - 16:39:40.735 INFO: 1 alignments done - 16:39:40.735 INFO: Alternative alignment: 1 - 16:39:40.858 INFO: 1 alignments done - 16:39:40.858 INFO: Alternative alignment: 2 - 16:39:40.858 INFO: Alternative alignment: 3 - 16:39:42.448 INFO: Premerge done - 16:39:42.448 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 16:39:42.575 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 Thu May 4 16:39:42 2023 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) - 16:39:42.663 INFO: Searching 1 column state sequences. - 16:39:42.808 INFO: Thread 0 query.a3m - 16:39:42.852 INFO: query.a3m is in A2M, A3M or FASTA format - 16:39:42.906 INFO: Iteration 1 - 16:39:44.995 INFO: Prefiltering database - 16:39:47.103 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 16:39:47.113 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 16:39:47.113 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 16:39:47.113 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 16:39:47.202 INFO: Alternative alignment: 0 - 16:39:47.320 INFO: 1 alignments done - 16:39:47.320 INFO: Alternative alignment: 1 - 16:39:47.434 INFO: 1 alignments done - 16:39:47.434 INFO: Alternative alignment: 2 - 16:39:47.434 INFO: Alternative alignment: 3 - 16:39:49.666 INFO: Premerge done - 16:39:49.666 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 16:39:49.763 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 16:39:50.023 INFO: query.a3m is in A2M, A3M or FASTA format - 16:39:50.074 INFO: Searching 1 database HHMs without prefiltering - 16:39:50.074 INFO: Iteration 1 - 16:39:51.402 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 16:39:51.569 INFO: Alternative alignment: 0 - 16:39:51.685 INFO: 1 alignments done - 16:39:51.685 INFO: Alternative alignment: 1 - 16:39:51.802 INFO: 1 alignments done - 16:39:51.802 INFO: Alternative alignment: 2 - 16:39:51.802 INFO: Alternative alignment: 3 - 16:39:53.410 INFO: Premerge done - 16:39:53.411 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 16:39:53.545 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 Thu May 4 16:39:53 2023 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) - 16:39:53.777 INFO: Thread 0 query.a3m - 16:39:53.821 INFO: query.a3m is in A2M, A3M or FASTA format - 16:39:53.873 INFO: Searching 1 database HHMs without prefiltering - 16:39:53.873 INFO: Iteration 1 - 16:39:55.842 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 16:39:55.931 INFO: Alternative alignment: 0 - 16:39:56.049 INFO: 1 alignments done - 16:39:56.049 INFO: Alternative alignment: 1 - 16:39:56.163 INFO: 1 alignments done - 16:39:56.163 INFO: Alternative alignment: 2 - 16:39:56.163 INFO: Alternative alignment: 3 - 16:39:58.295 INFO: Premerge done - 16:39:58.295 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 16:39:58.399 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 -j3 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 -j3 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 dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhfilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhmake contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_ca3m contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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_armhf.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-7_armhf.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_armhf.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-7_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/9287 and its subdirectories I: Current time: Thu May 4 16:42:54 -12 2023 I: pbuilder-time-stamp: 1683261774