I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 17 13:19:05 +14 2025 I: pbuilder-time-stamp: 1737069545 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hhsuite_3.3.0+ds-8.dsc] I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: unsupported subcommand dpkg-source: info: extracting hhsuite in hhsuite-3.3.0+ds dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.3.0+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_without_mpi dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying python3 dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying exe_suffix dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/449/tmp/hooks/D01_modify_environment starting debug: Running on virt32b. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 16 23:19 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/449/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/449/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=3ec3605fd9194634bb41bdaee16ea57f LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=449 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/pbuilderrc_UxIK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/b2 --logfile b2/build.log hhsuite_3.3.0+ds-8.dsc' SUDO_GID=112 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/449/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 ... 19566 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-7-common{a} imagemagick-7.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0t64{a} libgnutls30t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libidn2-0{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-7.q16-10{a} libmagickwand-7.q16-10{a} libnghttp2-14{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libraw23t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsimde-dev{a} libssh2-1t64{a} libtasn1-6{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-urw-base35 ghostscript krb5-locales libarchive-cpio-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmagickcore-7.q16-10-extra libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx netpbm psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 45.4 MB of archives. After unpacking 168 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf liblocale-gettext-perl armhf 1.07-7+b1 [14.7 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libfftw3-double3 armhf 3.3.10-2+b1 [330 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-2 [317 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-2 [371 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.5.0-0.1 [114 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libdav1d7 armhf 1.5.0-1+b1 [250 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libheif-plugin-dav1d armhf 1.19.5-1 [10.9 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libde265-0 armhf 1.0.15-1+b2 [145 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libheif-plugin-libde265 armhf 1.19.5-1 [14.3 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libheif1 armhf 1.19.5-1 [432 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.16-2 [131 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.82.4-1 [1327 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf liblqr-1-0 armhf 0.4.2-2.1+b2 [23.5 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.5.4-2 [412 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libopenjp2-7 armhf 2.5.0-2+b4 [179 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libraw23t64 armhf 0.21.3-1+b1 [370 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.5.0-0.1 [273 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libwebpdemux2 armhf 1.5.0-0.1 [112 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libwebpmux3 armhf 1.5.0-0.1 [123 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.10-2 [337 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b3 [45.2 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [67.4 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libmagickcore-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [1639 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libmagickwand-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [300 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-6 [56.0 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-6 [864 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-4 [196 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-13 [84.7 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-4 [723 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf cmake-data all 3.31.3-1 [2268 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 66 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.19+dfsg-1 [163 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.1-1 [303 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf cmake armhf 3.31.3-1 [5899 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.23 [90.6 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 91 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-4 [1489 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf help2man armhf 1.49.3 [198 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf imagemagick-7.q16 armhf 8:7.1.1.43+dfsg1-1 [726 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf imagemagick armhf 8:7.1.1.43+dfsg1-1 [20.0 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libsimde-dev all 0.8.2-2 [467 kB] Fetched 45.4 MB in 1s (35.7 MB/s) Preconfiguring packages ... 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 ... 19566 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7+b1_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libfftw3-double3:armhf. Preparing to unpack .../001-libfftw3-double3_3.3.10-2+b1_armhf.deb ... Unpacking libfftw3-double3:armhf (3.3.10-2+b1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../002-libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../003-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:armhf. Preparing to unpack .../004-libpng16-16t64_1.6.44-3_armhf.deb ... Unpacking libpng16-16t64:armhf (1.6.44-3) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 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Setting up libsharpyuv0:armhf (1.5.0-0.1) ... Setting up libxau6:armhf (1:1.0.11-1) ... Setting up libxdmcp6:armhf (1:1.1.5-1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libxcb1:armhf (1.17.0-2+b1) ... Setting up libicu72:armhf (72.1-6) ... Setting up liblerc4:armhf (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-13) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libuv1t64:armhf (1.48.0-7) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-4) ... Setting up m4 (1.4.19-5) ... Setting up libcom-err2:armhf (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:armhf (2.1-6.1+b2) ... 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Processing triggers for libc-bin (2.40-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/449/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/449/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (6.7s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 cd mybuild && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP -- Configuring done (9.2s) -- Generating done (0.4s) -- Build files have been written to: /build/reproducible-path/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild cd mybuild && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd 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make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f 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/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 2%] Generating ../generated/context_data.crf.h [ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated [ 3%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c: In function 'ffindex_index_parse': /build/reproducible-path/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 [ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 6%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 6%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 8%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp [ 9%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.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/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 11%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 11%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 12%] Generating ../generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h /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/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 12%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 13%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:42: 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/reproducible-path/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 [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc [ 15%] Linking C executable ffindex_apply cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 15%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 16%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 17%] Linking C executable ffindex_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 17%] 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/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 19%] Linking C executable ffindex_build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 [ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 20%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 22%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 22%] Built target ffindex_from_fasta [ 23%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 24%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/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/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 24%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 26%] Linking C executable ffindex_get cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_get.dir/link.d CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 27%] Built target ffindex_get [ 27%] Generating ../generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 28%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 29%] Built target generated make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 30%] Linking C executable ffindex_modify cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 32%] Linking C executable ffindex_unpack cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 [ 33%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 33%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" [ 33%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 34%] Linking C executable ffindex_order [ 35%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 36%] Built target ffindex_order make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 38%] Linking C executable ffindex_from_fasta_with_split cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 38%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 39%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 40%] Linking CXX executable a3m_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract.dir/link.d CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 40%] 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/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 42%] Linking CXX executable a3m_reduce [ 42%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 43%] Linking CXX executable a3m_database_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce.dir/link.d CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 43%] 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/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce.dir/link.d CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Built target a3m_database_reduce [ 45%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc [ 46%] Linking CXX executable a3m_database_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract.dir/link.d CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 46%] Built target a3m_database_extract [ 47%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc [ 48%] Linking CXX executable a3m_database_filter cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter.dir/link.d CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 48%] Built target a3m_database_filter [ 49%] Linking CXX static library libCS_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 49%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function 'int sprintf(char*, const char*, ...)', inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/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 ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/hhsuite-3.3.0+ds/lib/simd/simd.h:9, from /build/reproducible-path/hhsuite-3.3.0+ds/src/util.h:23, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.h:8, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.h:17, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp:8: /usr/include/c++/14/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++/14/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, | ^~~~~~~~~~~~~ /usr/include/c++/14/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++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp /usr/include/c++/14/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++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1589 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/14/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++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 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++/14/bits/stl_algo.h:1884:27: /usr/include/c++/14/bits/stl_algo.h:1868:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1868 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/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++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __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++/14/bits/stl_algo.h:4805:18, 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/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __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++/14/bits/stl_algo.h:1908:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = comparePair]' at /usr/include/c++/14/bits/stl_algo.h:4805:18, 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/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12: /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd 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-g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 82%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd 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-I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 88%] Linking CXX executable hhmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 [ 89%] Linking CXX executable hhfilter cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake.dir/link.d CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 89%] Built target hhmake make -f src/CMakeFiles/cstranslate.dir/build.make 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-I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter.dir/link.d CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 90%] Built target hhfilter make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 91%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 92%] Linking CXX executable hhalign cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign.dir/link.d CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 92%] Built target hhalign make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 93%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp [ 95%] Linking CXX executable hhconsensus cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus.dir/link.d CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp.dir/link.d CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 95%] Built target hhconsensus [ 95%] Built target hhblits_omp make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 96%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhsearch_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp.dir/link.d CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] Built target hhsearch_omp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX executable hhblits_ca3m cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 [100%] Linking CXX executable hhalign_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m.dir/link.d CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_ca3m /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp.dir/link.d CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhalign_omp [100%] Linking CXX executable cstranslate cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate.dir/link.d CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[4]: Nothing to be done for 'data/CMakeFiles/generated.dir/build'. make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src:/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh - 23:28:03.158 INFO: query.a3m is in A2M, A3M or FASTA format - 23:28:04.812 INFO: Alternative alignment: 0 - 23:28:05.072 INFO: 1 alignments done - 23:28:05.203 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 Jan 16 23:28:05 2025 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 1312 0 query.a3m 0 32666 11 0 query.a3m 0 32666 336 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 23:28:10.584 INFO: Searching 1 column state sequences. - 23:28:10.803 INFO: query.a3m is in A2M, A3M or FASTA format - 23:28:10.897 INFO: Iteration 1 - 23:28:12.182 INFO: Prefiltering database - 23:28:13.473 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:28:13.485 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:28:13.486 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:28:13.486 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:28:13.689 INFO: Alternative alignment: 0 - 23:28:13.948 INFO: 1 alignments done - 23:28:13.948 INFO: Alternative alignment: 1 - 23:28:14.202 INFO: 1 alignments done - 23:28:14.212 INFO: Alternative alignment: 2 - 23:28:14.212 INFO: Alternative alignment: 3 - 23:28:15.806 INFO: Premerge done - 23:28:15.807 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:28:15.973 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 Jan 16 23:28:15 2025 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) - 23:28:16.215 INFO: Searching 1 column state sequences. - 23:28:16.420 INFO: Thread 0 query.a3m - 23:28:16.481 INFO: query.a3m is in A2M, A3M or FASTA format - 23:28:16.574 INFO: Iteration 1 - 23:28:19.169 INFO: Prefiltering database - 23:28:21.783 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:28:21.801 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:28:21.801 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:28:21.801 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:28:21.905 INFO: Alternative alignment: 0 - 23:28:22.157 INFO: 1 alignments done - 23:28:22.157 INFO: Alternative alignment: 1 - 23:28:22.408 INFO: 1 alignments done - 23:28:22.408 INFO: Alternative alignment: 2 - 23:28:22.409 INFO: Alternative alignment: 3 - 23:28:25.305 INFO: Premerge done - 23:28:25.305 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:28:25.430 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 23:28:25.762 INFO: query.a3m is in A2M, A3M or FASTA format - 23:28:25.856 INFO: Searching 1 database HHMs without prefiltering - 23:28:25.856 INFO: Iteration 1 - 23:28:27.232 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:28:27.440 INFO: Alternative alignment: 0 - 23:28:27.689 INFO: 1 alignments done - 23:28:27.690 INFO: Alternative alignment: 1 - 23:28:27.944 INFO: 1 alignments done - 23:28:27.944 INFO: Alternative alignment: 2 - 23:28:27.944 INFO: Alternative alignment: 3 - 23:28:29.605 INFO: Premerge done - 23:28:29.605 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:28:29.779 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 Jan 16 23:28:29 2025 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) - 23:28:30.088 INFO: Thread 0 query.a3m - 23:28:30.145 INFO: query.a3m is in A2M, A3M or FASTA format - 23:28:30.238 INFO: Searching 1 database HHMs without prefiltering - 23:28:30.238 INFO: Iteration 1 - 23:28:32.837 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:28:32.937 INFO: Alternative alignment: 0 - 23:28:33.193 INFO: 1 alignments done - 23:28:33.194 INFO: Alternative alignment: 1 - 23:28:33.464 INFO: 1 alignments done - 23:28:33.465 INFO: Alternative alignment: 2 - 23:28:33.465 INFO: Alternative alignment: 3 - 23:28:36.274 INFO: Premerge done - 23:28:36.275 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:28:36.395 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild cd mybuild && make -j4 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j4 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_installman -Nhhsuite dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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/hhalign_omp 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/reproducible-path/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-2), " make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_armhf.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_armhf.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_armhf.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_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: user script /srv/workspace/pbuilder/449/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/449/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/449 and its subdirectories I: Current time: Fri Jan 17 13:32:22 +14 2025 I: pbuilder-time-stamp: 1737070342