Thu Jan 16 22:53:03 UTC 2025 I: starting to build hhsuite/trixie/armhf on jenkins on '2025-01-16 22:52' Thu Jan 16 22:53:03 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_12/11710/console.log Thu Jan 16 22:53:03 UTC 2025 I: Downloading source for trixie/hhsuite=3.3.0+ds-8 --2025-01-16 22:53:03-- http://deb.debian.org/debian/pool/main/h/hhsuite/hhsuite_3.3.0%2bds-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2271 (2.2K) [text/prs.lines.tag] Saving to: ‘hhsuite_3.3.0+ds-8.dsc’ 0K .. 100% 396M=0s 2025-01-16 22:53:03 (396 MB/s) - ‘hhsuite_3.3.0+ds-8.dsc’ saved [2271/2271] Thu Jan 16 22:53:03 UTC 2025 I: hhsuite_3.3.0+ds-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hhsuite Binary: hhsuite, hhsuite-data Architecture: any all Version: 3.3.0+ds-8 Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille , Sascha Steinbiss Homepage: https://toolkit.tuebingen.mpg.de/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/hhsuite Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man Package-List: hhsuite deb science optional arch=any hhsuite-data deb science optional arch=all Checksums-Sha1: d90462ba593366296d8916e184b42325caa4201b 4775072 hhsuite_3.3.0+ds.orig.tar.xz 0c6aa80d717ee79df31a05f33d2f461b1b6f0c88 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Checksums-Sha256: a81037f2e2a4801f1a42f5aa5939334fe038053d05ceabdc0899fefb8cc00a44 4775072 hhsuite_3.3.0+ds.orig.tar.xz d408a3d42581737068f06b96cd922c462f672beeb4faf94f41ac37340170b3cb 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Files: d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz 81b05abfd099550bfb153063e218961e 16868 hhsuite_3.3.0+ds-8.debian.tar.xz Dgit: 140af672217dfdd27cb9e04f647e16721cab7092 debian archive/debian/3.3.0+ds-8 https://git.dgit.debian.org/hhsuite -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmTYqGkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoEMA/+LuZTmLibgbYZApaOGZdaX+PkhrsA zfcKaSk3+e/HPlWNU154xxOVy+O+Y5pCo/EknRdiMEmQPW4Xp5CJOKEFkJE98rpu zorYV6MrnGZbtce76kYae9bIOO7ufuZgOmJQmC8o4Br1ARVzcdb0CoeT/I/YlUaO 1GeZ7FRxPV5+2FnJepnZtN3pVs9flLqfmjkTUpuXunVczXQ/9OqQDHLl+9FRuW9l G/rWE7wu1PZC12UYSIOaCP5ZLWBdD8aTCrD787zdv7NEdhH19LJmrpNiaV9pUmbn 1gWsCwnOkTJPw49XsA6PmabKG3eigVh/vX9OPCyUIFlwsgWk1j59a6iuRdVfKKec tu6iS43HxaDNpmr9RDMPwRy0IJyzFVVfefcFEkiq81xvXWeCyZaIMZG1jiprbitC n17iBZeZbuSNpVfwA8afeBsxfEQF5mMa14pv0b1tYMxFySu578muNQulSbVHRyIm U1EV7JmoLcrAdNisorrWjHxsreQpWDWoTtttMhQiHGRAqusHl3AfNChpj1VdctFp DLSXPJR57EGgm6Wh/l/dcAsYsoTRxoZwIslbpyajyZLIMgJsBYXU+aQyAnnix+KN OKWs50hmPC09YXC7cia0qp2IlQaR/Si5jpY2nDoxi115qKH1z6k+s49gHHEXcZGP OCf9WhUaFjSQ0Yk= =W1CO -----END PGP SIGNATURE----- Thu Jan 16 22:53:03 UTC 2025 I: Checking whether the package is not for us Thu Jan 16 22:53:03 UTC 2025 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Thu Jan 16 22:53:03 UTC 2025 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Thu Jan 16 23:18:57 UTC 2025 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 16 10:53:09 -12 2025 I: pbuilder-time-stamp: 1737067989 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/25080/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='7acace8beb264b688bb7815ab83bb85a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='25080' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/pbuilderrc_TxcZ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/b1 --logfile b1/build.log hhsuite_3.3.0+ds-8.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64a 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/25080/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 2s (19.8 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) ... 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Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../061-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../062-libcom-err2_1.47.2-1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.2-1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../063-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../064-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../065-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../066-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../067-libunistring5_1.3-1_armhf.deb ... Unpacking libunistring5:armhf (1.3-1) ... Selecting previously unselected package libidn2-0:armhf. Preparing to unpack .../068-libidn2-0_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-0:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:armhf. Preparing to unpack .../069-libp11-kit0_0.25.5-3_armhf.deb ... Unpacking libp11-kit0:armhf (0.25.5-3) ... Selecting previously unselected package libtasn1-6:armhf. Preparing to unpack .../070-libtasn1-6_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:armhf. Preparing to unpack .../071-libgnutls30t64_3.8.8-2_armhf.deb ... Unpacking libgnutls30t64:armhf (3.8.8-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. 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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../078-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl4t64:armhf. Preparing to unpack .../079-libcurl4t64_8.11.1-1_armhf.deb ... Unpacking libcurl4t64:armhf (8.11.1-1) ... Selecting previously unselected package libjsoncpp26:armhf. Preparing to unpack .../080-libjsoncpp26_1.9.6-3_armhf.deb ... Unpacking libjsoncpp26:armhf (1.9.6-3) ... Selecting previously unselected package librhash1:armhf. Preparing to unpack .../081-librhash1_1.4.5-1_armhf.deb ... Unpacking librhash1:armhf (1.4.5-1) ... Selecting previously unselected package libuv1t64:armhf. Preparing to unpack .../082-libuv1t64_1.48.0-7_armhf.deb ... Unpacking libuv1t64:armhf (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../083-cmake_3.31.3-1_armhf.deb ... 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Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 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: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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. 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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 (5.1s) -- Generating done (0.9s) -- 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 -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds 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Generating ../generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/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 [ 2%] 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 [ 3%] 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 [ 4%] 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 [ 5%] 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' [ 5%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[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]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 6%] 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 [ 7%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.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' [ 7%] Built target hhviterbialgorithm_with_celloff 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' [ 8%] 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 cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h [ 9%] 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 [ 10%] 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' [ 10%] Built target hhviterbialgorithm_with_celloff_and_ss [ 11%] Generating ../generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h 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' [ 12%] 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 [ 13%] 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 [ 14%] 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 [ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake 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 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/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' [ 15%] Built target hhviterbialgorithm_and_ss 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' [ 15%] 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.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 15%] Built target generated 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' [ 16%] 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 [ 17%] 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 [ 18%] Linking C executable ffindex_apply cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /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' [ 18%] 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' [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 /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)) | ^~~~~~~ [ 20%] Linking C executable ffindex_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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' [ 20%] 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' [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 [ 22%] Linking C executable ffindex_build cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 /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' [ 22%] Built target ffindex_build [ 23%] 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 [ 24%] 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 [ 25%] 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' [ 25%] Built target A3M_COMPRESS 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' [ 26%] 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 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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' [ 28%] 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 [ 29%] 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 /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' [ 29%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 30%] 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 [ 31%] Linking C executable ffindex_modify cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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' [ 32%] 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 [ 32%] Built target ffindex_modify 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' [ 33%] 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 [ 34%] 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 /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' [ 34%] Built target ffindex_unpack 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 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 [ 36%] Linking C executable ffindex_order cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 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 -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' [ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 [ 39%] 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' [ 39%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/build/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' [ 40%] 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 [ 41%] 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' [ 41%] Built target a3m_extract 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' [ 42%] 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 [ 43%] 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 [ 44%] Linking CXX executable a3m_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 44%] Built target CS_OBJECTS 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' [ 45%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 /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' [ 45%] Built target a3m_reduce make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend make[4]: Entering directory '/build/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' [ 46%] 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 [ 47%] Linking CXX executable a3m_database_reduce cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 /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' [ 47%] Built target a3m_database_reduce make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/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' [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 [ 49%] Linking CXX executable a3m_database_extract cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 /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' [ 49%] Built target a3m_database_extract [ 50%] 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/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o 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a3m_database_filter [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 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-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 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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 /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 ()); | ~~~~~~~~~~~~~~~~~ [ 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 [ 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 /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 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' 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' 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 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CMakeFiles/hhsearch.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 85%] 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/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 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 89%] Linking CXX executable hhsearch cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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.dir/link.d CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 89%] Built target hhsearch make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.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/cstranslate.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 90%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o cd 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/build/reproducible-path/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 91%] Linking CXX executable hhalign cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /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' [ 91%] Built target hhalign 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' [ 92%] 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 [ 93%] Linking CXX executable hhconsensus cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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' [ 93%] Built target hhconsensus 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' [ 94%] 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 ()); | ~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable hhblits_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 hhblits_omp make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.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' [ 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 /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 ()); | ~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable hhsearch_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /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' [ 97%] Built target hhsearch_omp make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend make[4]: Entering directory '/build/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/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' [ 98%] 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 ()); | ~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX executable hhalign_omp cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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' [ 99%] Built target hhalign_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 ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 [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 -j3 "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 - 23:10:49.281 INFO: query.a3m is in A2M, A3M or FASTA format - 23:10:51.937 INFO: Alternative alignment: 0 - 23:10:52.221 INFO: 1 alignments done - 23:10:52.402 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 23:10:52 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 2515 0 query.a3m 0 32666 11 0 query.a3m 0 32666 598 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 23:11:00.583 INFO: Searching 1 column state sequences. - 23:11:00.957 INFO: query.a3m is in A2M, A3M or FASTA format - 23:11:01.052 INFO: Iteration 1 - 23:11:03.205 INFO: Prefiltering database - 23:11:05.515 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:11:05.527 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:11:05.528 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:11:05.528 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:11:05.832 INFO: Alternative alignment: 0 - 23:11:06.198 INFO: 1 alignments done - 23:11:06.199 INFO: Alternative alignment: 1 - 23:11:06.645 INFO: 1 alignments done - 23:11:06.646 INFO: Alternative alignment: 2 - 23:11:06.646 INFO: Alternative alignment: 3 - 23:11:09.310 INFO: Premerge done - 23:11:09.311 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:11:09.482 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 23:11:09 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) - 23:11:09.619 INFO: Searching 1 column state sequences. - 23:11:09.968 INFO: Thread 0 query.a3m - 23:11:10.053 INFO: query.a3m is in A2M, A3M or FASTA format - 23:11:10.147 INFO: Iteration 1 - 23:11:13.661 INFO: Prefiltering database - 23:11:16.866 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 23:11:16.876 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 23:11:16.877 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 23:11:16.877 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:11:16.983 INFO: Alternative alignment: 0 - 23:11:17.372 INFO: 1 alignments done - 23:11:17.377 INFO: Alternative alignment: 1 - 23:11:17.658 INFO: 1 alignments done - 23:11:17.659 INFO: Alternative alignment: 2 - 23:11:17.659 INFO: Alternative alignment: 3 - 23:11:21.219 INFO: Premerge done - 23:11:21.220 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:11:21.417 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 23:11:21.966 INFO: query.a3m is in A2M, A3M or FASTA format - 23:11:22.058 INFO: Searching 1 database HHMs without prefiltering - 23:11:22.059 INFO: Iteration 1 - 23:11:24.208 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:11:24.603 INFO: Alternative alignment: 0 - 23:11:24.938 INFO: 1 alignments done - 23:11:24.945 INFO: Alternative alignment: 1 - 23:11:25.225 INFO: 1 alignments done - 23:11:25.229 INFO: Alternative alignment: 2 - 23:11:25.230 INFO: Alternative alignment: 3 - 23:11:28.010 INFO: Premerge done - 23:11:28.011 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:11:28.258 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 23:11:28 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) - 23:11:28.810 INFO: Thread 0 query.a3m - 23:11:28.942 INFO: query.a3m is in A2M, A3M or FASTA format - 23:11:29.108 INFO: Searching 1 database HHMs without prefiltering - 23:11:29.108 INFO: Iteration 1 - 23:11:32.372 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 23:11:32.562 INFO: Alternative alignment: 0 - 23:11:32.900 INFO: 1 alignments done - 23:11:32.900 INFO: Alternative alignment: 1 - 23:11:33.261 INFO: 1 alignments done - 23:11:33.261 INFO: Alternative alignment: 2 - 23:11:33.262 INFO: Alternative alignment: 3 - 23:11:36.688 INFO: Premerge done - 23:11:36.693 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 23:11:36.837 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 -j3 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 -j3 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_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign 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-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_armhf.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: 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/25080 and its subdirectories I: Current time: Thu Jan 16 11:17:19 -12 2025 I: pbuilder-time-stamp: 1737069439 Thu Jan 16 23:18:59 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Thu Jan 16 23:18:59 UTC 2025 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Thu Jan 16 23:33:19 UTC 2025 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Thu Jan 16 23:33:22 UTC 2025 I: hhsuite_3.3.0+ds-8_armhf.changes: Format: 1.8 Date: Sun, 13 Aug 2023 10:47:11 +0200 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: all armhf Version: 3.3.0+ds-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: hhsuite - sensitive protein sequence searching based on HMM-HMM alignment hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment ( Closes: 1037689 Changes: hhsuite (3.3.0+ds-8) unstable; urgency=medium . * Team upload. * gcc-13.patch: new: fix ftbfs with gcc 13. (Closes: #1037689) * d/control: declare compliance to standards version 4.6.2. Checksums-Sha1: 262e7be5b83dc9c81fc3723d97e7a6f2828ad07f 4402152 hhsuite-data_3.3.0+ds-8_all.deb fde21b276105a621cc7710a47271f08ee6bd97a7 18278540 hhsuite-dbgsym_3.3.0+ds-8_armhf.deb 706d382374ed6cf92a1b251c3dfa608f70f686ec 7421 hhsuite_3.3.0+ds-8_armhf.buildinfo 1d1cad22db886bfdea1dfab8b6b3af844e0293e8 10429384 hhsuite_3.3.0+ds-8_armhf.deb Checksums-Sha256: a63b9845bb3133774e061b97e68ea55d257a970f86cf588d8f4f3123558839a5 4402152 hhsuite-data_3.3.0+ds-8_all.deb c868a42d82f9452e1884a79b6b6d4d7ce735cc6f5242a4da55f9fb5176c60b1c 18278540 hhsuite-dbgsym_3.3.0+ds-8_armhf.deb 6d5277e89ab183cdb75488b806d5b70d5de4b342394cc19a9eeb998985f6291e 7421 hhsuite_3.3.0+ds-8_armhf.buildinfo 5c7a17f2708a51bee3ed0eaac97f22518e47db81b7aad322e8602829e7ac37cc 10429384 hhsuite_3.3.0+ds-8_armhf.deb Files: c9b8c4baaf198c024d9f15d0e5ed4ffa 4402152 science optional hhsuite-data_3.3.0+ds-8_all.deb 4170e16bbd5571a9cdd1db6a6009bd5a 18278540 debug optional hhsuite-dbgsym_3.3.0+ds-8_armhf.deb 4530666c918bedae02d4e24c3f2da66c 7421 science optional hhsuite_3.3.0+ds-8_armhf.buildinfo f92a48fd6b7f30852e52ecd0e414ebc6 10429384 science optional hhsuite_3.3.0+ds-8_armhf.deb Thu Jan 16 23:33:23 UTC 2025 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_12-11710.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/hhsuite_3.3.0+ds-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/hhsuite_3.3.0+ds-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/hhsuite_3.3.0+ds-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/b1/hhsuite_3.3.0+ds-8_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.kUbUlqwa/b2/hhsuite_3.3.0+ds-8_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.775s) 0.775s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.378s) 0.378s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.117s CPU time consumed: 1.041s Thu Jan 16 23:33:27 UTC 2025 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Thu Jan 16 23:33:27 UTC 2025 I: hhsuite from trixie built successfully and reproducibly on armhf. Thu Jan 16 23:33:28 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Jan 16 23:33:28 UTC 2025 I: Submitting 12K b1/hhsuite_3.3.0+ds-8_armhf.buildinfo.asc Thu Jan 16 23:33:29 UTC 2025 I: Submitting 12K b2/hhsuite_3.3.0+ds-8_armhf.buildinfo.asc Thu Jan 16 23:33:29 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jan 16 23:33:29 UTC 2025 I: Done submitting .buildinfo files. Thu Jan 16 23:33:29 UTC 2025 I: Removing signed hhsuite_3.3.0+ds-8_armhf.buildinfo.asc files: removed './b1/hhsuite_3.3.0+ds-8_armhf.buildinfo.asc' removed './b2/hhsuite_3.3.0+ds-8_armhf.buildinfo.asc'