sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | hhsuite 3.3.0+ds-8 (amd64) Tue, 21 Jan 2025 03:54:17 +0000 | +==============================================================================+ Package: hhsuite Version: 3.3.0+ds-8 Source Version: 3.3.0+ds-8 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 21 Jan 2025 03:54:17 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hhsuite_3.3.0+ds-8 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hhsuite_3.3.0+ds-8 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 21 Jan 2025 03:54:18 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:3 http://localhost:3142/debian sid InRelease [205 kB] Get:4 http://deb.debian.org/debian unstable InRelease [205 kB] Get:5 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [68.8 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [66.7 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [68.8 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [66.7 kB] Fetched 673 kB in 7s (98.3 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 21 Jan 2025 03:54:26 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/hhsuite_3.3.0+ds-8.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 21 Jan 2025 03:54:26 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man, build-essential Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ InRelease Get:2 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ Release [609 B] Ign:3 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ Release.gpg Get:4 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ Sources [644 B] Get:5 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ Packages [683 B] Fetched 1936 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base help2man hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl libarchive13t64 libbrotli1 libcom-err2 libcurl4t64 libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0t64 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libicu72 libjbig0 libjpeg62-turbo libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16t64 libproc2-0 libpsl5t64 libraw23t64 librhash1 librtmp1 libsharpyuv0 libsimde-dev libssh2-1t64 libtiff6 libtool libuchardet0 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db po-debconf procps sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff imagemagick-7-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils texlive-base-bin transfig libraw-bin xdg-utils lrzip libfftw3-bin libfftw3-dev low-memory-monitor krb5-doc krb5-user libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar libheif-plugin-rav1e libheif-plugin-svtenc liblcms2-utils libmagickcore-7.q16-10-extra libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libmagickcore-7.q16-10-extra ghostscript netpbm ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libheif-plugin-x265 libheif-plugin-aomenc krb5-locales fonts-urw-base35 publicsuffix libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base help2man hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl libarchive13t64 libbrotli1 libcom-err2 libcurl4t64 libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0t64 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libicu72 libjbig0 libjpeg62-turbo libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16t64 libproc2-0 libpsl5t64 libraw23t64 librhash1 librtmp1 libsharpyuv0 libsimde-dev libssh2-1t64 libtiff6 libtool libuchardet0 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db po-debconf procps sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 51.8 MB of archives. After this operation, 188 MB of additional disk space will be used. Get:1 copy:/build/hhsuite-r2mgi3/resolver-wS9qU4/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [884 B] Get:2 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.45-1 [281 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:11 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libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libraw23t64 amd64 0.21.3-1+b1 [390 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:32 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bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.4-2 [2267 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:66 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.4-2 [12.0 MB] Get:77 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:83 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 imagemagick-7.q16 amd64 8:7.1.1.43+dfsg1-1 [726 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 imagemagick amd64 8:7.1.1.43+dfsg1-1 [20.0 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Preconfiguring packages ... Fetched 51.8 MB in 0s (130 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../01-libfftw3-double3_3.3.10-2+b1_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2+b1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../02-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../03-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../04-libpng16-16t64_1.6.45-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.45-1) ... 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Setting up libexpat1:amd64 (2.6.4-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-2) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.4-1) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.45-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libltdl7:amd64 (2.5.4-2) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libraw23t64:amd64 (0.21.3-1+b1) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.5.0-1+b1) ... Setting up liblqr-1-0:amd64 (0.4.2-2.1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up cmake-data (3.31.4-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libde265-0:amd64 (1.0.15-1+b2) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libcurl4t64:amd64 (8.11.1-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.31.4-2) ... Setting up debhelper (13.24.1) ... Setting up libheif-plugin-dav1d:amd64 (1.19.5-1) ... Setting up libheif1:amd64 (1.19.5-1) ... Setting up libmagickcore-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.5-1) ... Setting up libmagickwand-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 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) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 21 Jan 2025 03:54:35 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Tue, 21 Jan 2025 03:54:35 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.23 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 cmake_3.31.4-2 cmake-data_3.31.4-2 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 fontconfig-config_2.15.0-2 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 help2man_1.49.3 hicolor-icon-theme_0.18-1 hostname_3.25 imagemagick_8:7.1.1.43+dfsg1-1 imagemagick-7-common_8:7.1.1.43+dfsg1-1 imagemagick-7.q16_8:7.1.1.43+dfsg1-1 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.23 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.43.50.20250108-1 libblkid1_2.40.4-1 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-14 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libcurl4t64_8.11.1-1+b1 libdav1d7_1.5.0-1+b1 libdb5.3t64_5.3.28+dfsg2-9 libde265-0_1.0.15-1+b2 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdeflate0_1.23-1+b1 libdpkg-perl_1.22.14 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libexpat1_2.6.4-1 libffi8_3.4.6-1 libfftw3-double3_3.3.10-2+b1 libfile-stripnondeterminism-perl_1.14.0-1 libfontconfig1_2.15.0-2 libfreetype6_2.13.3+dfsg-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libglib2.0-0t64_2.82.4-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libgssapi-krb5-2_1.21.3-4 libheif-plugin-dav1d_1.19.5-1 libheif-plugin-libde265_1.19.5-1 libheif1_1.19.5-1 libhogweed6t64_3.10-1+b1 libhwasan0_14.2.0-14 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-14 libjansson4_2.14-2+b3 libjbig0_2.1-6.1+b2 libjpeg62-turbo_1:2.1.5-3+b1 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-4 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-4 libkrb5support0_1.21.3-4 libksba8_1.6.7-2+b1 liblcms2-2_2.16-2 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.9+dfsg-1 liblerc4_4.0.0+ds-5 liblocale-gettext-perl_1.07-7+b1 liblqr-1-0_0.4.2-2.1+b2 liblsan0_14.2.0-14 libltdl7_2.5.4-2 liblz4-1_1.9.4-4 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmagickcore-7.q16-10_8:7.1.1.43+dfsg1-1 libmagickwand-7.q16-10_8:7.1.1.43+dfsg1-1 libmd0_1.1.0-2+b1 libmount1_2.40.4-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnpth0t64_1.8-2 libopenjp2-7_2.5.0-2+b4 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpcre2-8-0_10.44-5 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-1 libpipeline1_1.5.8-1 libpng16-16t64_1.6.45-1 libproc2-0_2:4.0.4-6 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-14 libraw23t64_0.21.3-1+b1 libreadline8t64_8.2-6 librhash1_1.4.5-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8+b1 libsasl2-modules-db_2.1.28+dfsg1-8+b1 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsharpyuv0_1.5.0-0.1 libsimde-dev_0.8.2-2 libsmartcols1_2.40.4-1 libsqlite3-0_3.46.1-1 libssh2-1t64_1.11.1-1 libssl3t64_3.4.0-2 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 libsystemd0_257.2-2 libtasn1-6_4.19.0-3+b3 libtiff6_4.5.1+git230720-5 libtinfo6_6.5-2+b1 libtool_2.5.4-2 libtsan2_14.2.0-14 libubsan1_14.2.0-14 libuchardet0_0.0.8-1+b2 libudev1_257.2-2 libunistring5_1.3-1 libuuid1_2.40.4-1 libuv1t64_1.48.0-7 libwebp7_1.5.0-0.1 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+------------------------------------------------------------------------------+ | Build Tue, 21 Jan 2025 03:54:35 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----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----- gpgv: Signature made Sun Aug 13 09:54:49 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting hhsuite in /build/hhsuite-r2mgi3/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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Tue, 21 Jan 2025 03:54:36 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hhsuite_3.3.0+ds-8 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hhsuite_3.3.0+ds-8 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-f662b39a-e9af-4413-a8a3-357551b6b693 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz 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 -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building hhsuite using existing ./hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building hhsuite in hhsuite_3.3.0+ds-8.debian.tar.xz dpkg-source: info: building hhsuite in hhsuite_3.3.0+ds-8.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ dh_auto_configure --builddirectory build_${SIMD} -- -DEXE_SUFFIX=-${SIMD} -DNATIVE_ARCH=0; \ done cd build_avx2 && 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/x86_64-linux-gnu -DEXE_SUFFIX=-avx2 -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 cd build_avx && 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/x86_64-linux-gnu -DEXE_SUFFIX=-avx -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx cd build_sse4.1 && 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/x86_64-linux-gnu -DEXE_SUFFIX=-sse4.1 -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 cd build_ssse3 && 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/x86_64-linux-gnu -DEXE_SUFFIX=-ssse3 -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (2.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 cd build_sse3 && 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/x86_64-linux-gnu -DEXE_SUFFIX=-sse3 -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (2.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" && \ dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain -DNATIVE_ARCH=0 cd build_plain && 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/x86_64-linux-gnu -DEXE_SUFFIX=-plain -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/hhsuite-r2mgi3/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/x86_64-linux-gnu -DNATIVE_ARCH=0 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_build --builddirectory build_${SIMD} ; \ done cd build_avx2 && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 1%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 4%] Built target ffindex [ 5%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" [ 6%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 7%] Built target generated make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a [ 10%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 10%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build [ 10%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 16%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 16%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 16%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/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)) | ^~~~~~~ [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 18%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 18%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 20%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 20%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking C executable ffindex_build cd 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc [ 26%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 28%] Linking C executable ffindex_from_fasta cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 28%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src 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-std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 30%] Linking C executable ffindex_get cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 30%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_modify cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 [ 33%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 33%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" /usr/bin/ar qc libCS_OBJECTS.a 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" [ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_unpack cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 38%] Linking C executable ffindex_order cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o.d -o 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src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 46%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhutil.cpp make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_reduce-avx2.dir/DependInfo.cmake "--color=" [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/util.cpp make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 52%] Building CXX object src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 53%] Linking CXX executable a3m_reduce-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx2.dir/link.d "CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 53%] Built target a3m_reduce-avx2 make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_reduce-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 54%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 55%] Linking CXX executable a3m_database_reduce-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-avx2.dir/link.d "CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 55%] Built target a3m_database_reduce-avx2 make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_extract-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 56%] Building CXX object src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 58%] Linking CXX executable a3m_database_extract-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-avx2.dir/link.d "CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 58%] Built target a3m_database_extract-avx2 make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_filter-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 59%] Building CXX object src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 60%] Linking CXX executable a3m_database_filter-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-avx2.dir/link.d "CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 60%] Built target a3m_database_filter-avx2 [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-avx2.dir/link.d "CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o" -o hhblits-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 82%] Built target hhblits-avx2 make -f src/CMakeFiles/hhfilter-avx2.dir/build.make 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hhfilter-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-avx2.dir/link.d "CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o" -o hhsearch-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 87%] Built target hhsearch-avx2 make -f 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp /usr/bin/c++ -g -O2 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhconsensus-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx2.dir/link.d "CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o" -o hhalign-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 90%] Built target hhalign-avx2 make -f src/CMakeFiles/cstranslate-avx2.dir/build.make src/CMakeFiles/cstranslate-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/cstranslate-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/cstranslate-avx2.dir/build.make src/CMakeFiles/cstranslate-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 91%] Building CXX object src/CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx2.dir/link.d "CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o" -o hhconsensus-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 92%] Built target hhconsensus-avx2 make -f src/CMakeFiles/hhblits_omp-avx2.dir/build.make src/CMakeFiles/hhblits_omp-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits_omp-avx2.dir/build.make src/CMakeFiles/hhblits_omp-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx2.dir/link.d "CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 94%] Built target hhblits_omp-avx2 make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhsearch_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-avx2.dir/link.d "CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 96%] Built target hhsearch_omp-avx2 make -f src/CMakeFiles/hhalign_omp-avx2.dir/build.make src/CMakeFiles/hhalign_omp-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhalign_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhalign_omp-avx2.dir/build.make src/CMakeFiles/hhalign_omp-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx2.dir/link.d "CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 98%] Built target hhalign_omp-avx2 make -f src/CMakeFiles/hhblits_ca3m-avx2.dir/build.make src/CMakeFiles/hhblits_ca3m-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_ca3m-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits_ca3m-avx2.dir/build.make src/CMakeFiles/hhblits_ca3m-avx2.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-avx2.dir/link.d "CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [100%] Built target hhblits_ca3m-avx2 [100%] Linking CXX executable cstranslate-avx2 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-avx2.dir/link.d "CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o" -o cstranslate-avx2 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' [100%] Built target cstranslate-avx2 make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd build_avx && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 4%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 [ 7%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 7%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 9%] Built target hhviterbialgorithm_with_celloff_and_ss [ 10%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 11%] Built target generated make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 15%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/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)) | ^~~~~~~ [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 17%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 20%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 20%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking C executable ffindex_build cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 24%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 26%] Linking C executable ffindex_from_fasta cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 26%] Built target ffindex_from_fasta [ 27%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc [ 28%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 30%] Linking C executable ffindex_get cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 30%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_modify cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_order cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 38%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 38%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_extract-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 39%] Building CXX object src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 40%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 40%] Built target CS_OBJECTS make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_reduce-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 41%] Building CXX object src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 42%] Linking CXX executable a3m_extract-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-avx.dir/link.d "CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o" -o a3m_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 42%] Built target a3m_extract-avx make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_reduce-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 43%] Linking CXX executable a3m_reduce-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx.dir/link.txt --verbose=1 [ 44%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx.dir/link.d "CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 44%] Built target a3m_reduce-avx make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_extract-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 45%] Building CXX object src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 46%] Linking CXX executable a3m_database_reduce-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-avx.dir/link.d "CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 46%] Built target a3m_database_reduce-avx make -f src/CMakeFiles/a3m_database_filter-avx.dir/build.make src/CMakeFiles/a3m_database_filter-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_filter-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_filter-avx.dir/build.make src/CMakeFiles/a3m_database_filter-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 47%] Building CXX object src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 48%] Linking CXX executable a3m_database_extract-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-avx.dir/link.d "CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 48%] Built target a3m_database_extract-avx make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.cpp [ 50%] Linking CXX executable a3m_database_filter-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-avx.dir/link.d "CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 50%] Built target a3m_database_filter-avx [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/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 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make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits-avx.dir/build.make src/CMakeFiles/hhblits-avx.dir/depend make -f src/CMakeFiles/hhmake-avx.dir/build.make src/CMakeFiles/hhmake-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits-avx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 86%] Linking CXX executable hhsearch-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx.dir/link.txt --verbose=1 [ 87%] Linking CXX executable hhfilter-avx cd 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hhsearch-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhalign-avx.dir/build.make src/CMakeFiles/hhalign-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 87%] Built target hhsearch-avx make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx 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-fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx.dir/link.d "CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o" -o hhalign-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 90%] Built target hhalign-avx make -f src/CMakeFiles/cstranslate-avx.dir/build.make src/CMakeFiles/cstranslate-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/cstranslate-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/cstranslate-avx.dir/build.make src/CMakeFiles/cstranslate-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 91%] Building CXX object src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx.dir/link.d "CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o" -o hhconsensus-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 92%] Built target hhconsensus-avx make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx.dir/link.d "CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 94%] Built target hhblits_omp-avx make -f src/CMakeFiles/hhsearch_omp-avx.dir/build.make src/CMakeFiles/hhsearch_omp-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhsearch_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhsearch_omp-avx.dir/build.make src/CMakeFiles/hhsearch_omp-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-avx.dir/link.d "CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 96%] Built target hhsearch_omp-avx make -f src/CMakeFiles/hhalign_omp-avx.dir/build.make src/CMakeFiles/hhalign_omp-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhalign_omp-avx.dir/build.make src/CMakeFiles/hhalign_omp-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx.dir/link.d "CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhalign_omp-avx make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_ca3m-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-avx.dir/link.d "CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [100%] Built target hhblits_ca3m-avx [100%] Linking CXX executable cstranslate-avx cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-avx.dir/link.d "CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o" -o cstranslate-avx libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' [100%] Built target cstranslate-avx make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd build_sse4.1 && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build [ 1%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 4%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 6%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h [ 8%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 [ 9%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 9%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 11%] Built target hhviterbialgorithm_and_ss [ 12%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/as.cc cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 14%] Built target generated make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/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)) | ^~~~~~~ [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 17%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 19%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 19%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking C executable ffindex_build cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 24%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 26%] Linking C executable ffindex_from_fasta cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 26%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 28%] Linking C executable ffindex_get cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 28%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 30%] Linking C executable ffindex_modify cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc [ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 34%] Linking C executable ffindex_unpack cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make 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CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 [ 37%] Linking C executable ffindex_order cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.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 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-ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 37%] Built target ffindex_order make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" [ 38%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 39%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 43%] Linking CXX executable a3m_extract-sse4.1 cd 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 45%] Linking CXX executable a3m_reduce-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-sse4.1.dir/link.d "CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 45%] Built target a3m_reduce-sse4.1 [ 46%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhit.cpp [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd 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Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -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 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src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 52%] Linking CXX executable a3m_database_reduce-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-sse4.1.dir/link.d "CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 52%] Built target a3m_database_reduce-sse4.1 make -f src/CMakeFiles/a3m_database_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_database_extract-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_database_extract-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f 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-D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 54%] Linking CXX executable a3m_database_extract-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic 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directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 55%] Building CXX object src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 56%] Linking CXX executable a3m_database_filter-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF 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-Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd 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src/CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 81%] Building CXX object src/CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time 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libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 82%] Built target hhblits-sse4.1 make -f src/CMakeFiles/hhfilter-sse4.1.dir/build.make src/CMakeFiles/hhfilter-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhfilter-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f 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cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 84%] Built target hhmake-sse4.1 make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make src/CMakeFiles/hhsearch-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make 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-Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-sse4.1.dir/link.d "CMakeFiles/hhfilter-sse4.1.dir/hhfilter.cpp.o" -o hhfilter-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 87%] Built target hhfilter-sse4.1 make -f src/CMakeFiles/hhalign-sse4.1.dir/build.make src/CMakeFiles/hhalign-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhalign-sse4.1.dir/build.make src/CMakeFiles/hhalign-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 88%] Building CXX object src/CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-sse4.1.dir/link.d "CMakeFiles/hhsearch-sse4.1.dir/hhblits_app.cpp.o" -o hhsearch-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 88%] Built target hhsearch-sse4.1 make -f src/CMakeFiles/hhconsensus-sse4.1.dir/build.make src/CMakeFiles/hhconsensus-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhconsensus-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f 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-fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-sse4.1.dir/link.d "CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o" -o hhalign-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 90%] Built target hhalign-sse4.1 make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/cstranslate-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 91%] Building CXX object src/CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-sse4.1.dir/link.d "CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o" -o hhconsensus-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 92%] Built target hhconsensus-sse4.1 make -f src/CMakeFiles/hhblits_omp-sse4.1.dir/build.make src/CMakeFiles/hhblits_omp-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhblits_omp-sse4.1.dir/build.make src/CMakeFiles/hhblits_omp-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse4.1.dir/link.d "CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 94%] Built target hhblits_omp-sse4.1 make -f src/CMakeFiles/hhsearch_omp-sse4.1.dir/build.make src/CMakeFiles/hhsearch_omp-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhsearch_omp-sse4.1.dir/build.make src/CMakeFiles/hhsearch_omp-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-sse4.1.dir/link.d "CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 96%] Built target hhsearch_omp-sse4.1 make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-sse4.1.dir/link.d "CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 98%] Built target hhalign_omp-sse4.1 make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_ca3m-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse4.1.dir/link.d "CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [100%] Built target hhblits_ca3m-sse4.1 [100%] Linking CXX executable cstranslate-sse4.1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-sse4.1.dir/link.d "CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o" -o cstranslate-sse4.1 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' [100%] Built target cstranslate-sse4.1 make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd build_ssse3 && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 1%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 4%] Built target ffindex [ 5%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend [ 6%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 6%] Built target generated make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script 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Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 11%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/as.cc [ 14%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 14%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/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)) | ^~~~~~~ [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 17%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 19%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 19%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 21%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 22%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 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lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 26%] Linking C executable ffindex_from_fasta cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory 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ffindex_get cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 28%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 30%] Linking C executable ffindex_modify cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 30%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src 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CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 32%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" [ 33%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make 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-o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 35%] Linking C executable ffindex_order cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 35%] 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 37%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 37%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_extract-ssse3.dir/build.make src/CMakeFiles/a3m_extract-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_extract-ssse3.dir/DependInfo.cmake "--color=" [ 38%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_extract-ssse3.dir/build.make src/CMakeFiles/a3m_extract-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc [ 39%] Building CXX object src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 40%] Linking CXX executable a3m_extract-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-ssse3.dir/link.d "CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o" -o a3m_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 40%] Built target a3m_extract-ssse3 make 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-DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 42%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 42%] Built target CS_OBJECTS make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_reduce-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 44%] Linking CXX executable a3m_reduce-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-ssse3.dir/link.d "CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 44%] Built target a3m_reduce-ssse3 make -f src/CMakeFiles/a3m_database_extract-ssse3.dir/build.make src/CMakeFiles/a3m_database_extract-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_extract-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_extract-ssse3.dir/build.make src/CMakeFiles/a3m_database_extract-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 45%] Building CXX object src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 46%] Linking CXX executable a3m_database_reduce-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_filter-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 47%] Building CXX object src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 48%] Linking CXX executable a3m_database_extract-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-ssse3.dir/link.d "CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 48%] Built target a3m_database_extract-ssse3 make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.cpp [ 50%] Linking CXX executable a3m_database_filter-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-ssse3.dir/link.d "CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 50%] Built target a3m_database_filter-ssse3 [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF 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-fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated 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CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/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 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-ssse3.dir/link.d "CMakeFiles/hhmake-ssse3.dir/hhmake.cpp.o" -o hhmake-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 84%] Built target hhmake-ssse3 make -f src/CMakeFiles/hhsearch-ssse3.dir/build.make src/CMakeFiles/hhsearch-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 86%] Linking CXX executable hhfilter-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-ssse3.dir/link.d "CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o" -o hhfilter-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 86%] Built target hhfilter-ssse3 make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 88%] Linking CXX executable hhsearch-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-ssse3.dir/link.d "CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o" -o hhsearch-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 88%] Built target hhsearch-ssse3 make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-ssse3.dir/link.d "CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o" -o hhalign-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 90%] Built target hhalign-ssse3 make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/cstranslate-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 91%] Building CXX object src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-ssse3.dir/link.d "CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o" -o hhconsensus-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 92%] Built target hhconsensus-ssse3 make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-ssse3.dir/link.d "CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 94%] Built target hhblits_omp-ssse3 make -f src/CMakeFiles/hhsearch_omp-ssse3.dir/build.make src/CMakeFiles/hhsearch_omp-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhsearch_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhsearch_omp-ssse3.dir/build.make src/CMakeFiles/hhsearch_omp-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-ssse3.dir/link.d "CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 96%] Built target hhsearch_omp-ssse3 make -f src/CMakeFiles/hhalign_omp-ssse3.dir/build.make src/CMakeFiles/hhalign_omp-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhalign_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhalign_omp-ssse3.dir/build.make src/CMakeFiles/hhalign_omp-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-ssse3.dir/link.d "CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 98%] Built target hhalign_omp-ssse3 make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_ca3m-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-ssse3.dir/link.d "CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target hhblits_ca3m-ssse3 [100%] Linking CXX executable cstranslate-ssse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-ssse3.dir/link.d "CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-ssse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target cstranslate-ssse3 make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd build_sse3 && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 4%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 6%] Built target hhviterbialgorithm_with_celloff [ 7%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h [ 8%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 9%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 9%] Built target generated make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 11%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 15%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/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)) | ^~~~~~~ [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 18%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 18%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 20%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 20%] Built target ffindex_apply [ 21%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc [ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 24%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 24%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 26%] Linking C executable ffindex_build cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 26%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 28%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 28%] Built target CS_OBJECTS make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o [ 29%] Linking C executable ffindex_from_fasta cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 31%] Linking C executable ffindex_get cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 [ 31%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src 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-ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 34%] Linking C executable ffindex_modify cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 35%] Linking C executable ffindex_unpack cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 [ 35%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src 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-ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 36%] Built target ffindex_unpack make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 37%] Linking C executable ffindex_order cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 38%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 38%] Built target ffindex_order make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 40%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 40%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 40%] Built target ffindex_from_fasta_with_split [ 41%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 42%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhit.cpp [ 43%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp make -f src/CMakeFiles/a3m_extract-sse3.dir/build.make src/CMakeFiles/a3m_extract-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_extract-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_extract-sse3.dir/build.make src/CMakeFiles/a3m_extract-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 44%] Building CXX object src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 45%] Linking CXX executable a3m_extract-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-sse3.dir/link.d "CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o" -o a3m_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 45%] Built target a3m_extract-sse3 make -f src/CMakeFiles/a3m_reduce-sse3.dir/build.make src/CMakeFiles/a3m_reduce-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_reduce-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_reduce-sse3.dir/build.make src/CMakeFiles/a3m_reduce-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 46%] Building CXX object src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 47%] Linking CXX executable a3m_reduce-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-sse3.dir/link.d "CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 47%] Built target a3m_reduce-sse3 make -f src/CMakeFiles/a3m_database_reduce-sse3.dir/build.make src/CMakeFiles/a3m_database_reduce-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_reduce-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_reduce-sse3.dir/build.make src/CMakeFiles/a3m_database_reduce-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 48%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 50%] Linking CXX executable a3m_database_reduce-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-sse3.dir/link.d "CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 50%] Built target a3m_database_reduce-sse3 make -f src/CMakeFiles/a3m_database_extract-sse3.dir/build.make src/CMakeFiles/a3m_database_extract-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_extract-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_extract-sse3.dir/build.make src/CMakeFiles/a3m_database_extract-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 51%] Building CXX object src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 52%] Linking CXX executable a3m_database_extract-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-sse3.dir/link.d "CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 52%] Built target a3m_database_extract-sse3 make -f src/CMakeFiles/a3m_database_filter-sse3.dir/build.make src/CMakeFiles/a3m_database_filter-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 54%] Linking CXX executable a3m_database_filter-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse3.dir/link.txt --verbose=1 [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalign.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-sse3.dir/link.d "CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 55%] Built target a3m_database_filter-sse3 [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ 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src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD 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-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && 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src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a 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../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 82%] Built target hhblits-sse3 make -f src/CMakeFiles/hhfilter-sse3.dir/build.make src/CMakeFiles/hhfilter-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhfilter-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhfilter-sse3.dir/build.make 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src/CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-sse3.dir/link.d "CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o" -o hhmake-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 84%] Built target hhmake-sse3 make -f src/CMakeFiles/hhsearch-sse3.dir/build.make src/CMakeFiles/hhsearch-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhsearch-sse3.dir/build.make src/CMakeFiles/hhsearch-sse3.dir/build make[4]: Entering directory 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libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 86%] Built target hhfilter-sse3 make -f src/CMakeFiles/hhalign-sse3.dir/build.make src/CMakeFiles/hhalign-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhalign-sse3.dir/build.make src/CMakeFiles/hhalign-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 87%] Linking CXX executable hhsearch-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse3.dir/link.txt --verbose=1 [ 88%] Building CXX object src/CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_app.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-sse3.dir/link.d "CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o" -o hhsearch-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 88%] Built target hhsearch-sse3 make -f src/CMakeFiles/hhconsensus-sse3.dir/build.make src/CMakeFiles/hhconsensus-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhconsensus-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhconsensus-sse3.dir/build.make src/CMakeFiles/hhconsensus-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-sse3.dir/link.d "CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o" -o hhalign-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 90%] Built target hhalign-sse3 make -f src/CMakeFiles/cstranslate-sse3.dir/build.make src/CMakeFiles/cstranslate-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/cstranslate-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/cstranslate-sse3.dir/build.make src/CMakeFiles/cstranslate-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 91%] Building CXX object src/CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-sse3.dir/link.d "CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o" -o hhconsensus-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 92%] Built target hhconsensus-sse3 make -f src/CMakeFiles/hhblits_omp-sse3.dir/build.make src/CMakeFiles/hhblits_omp-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhblits_omp-sse3.dir/build.make src/CMakeFiles/hhblits_omp-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse3.dir/link.d "CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 94%] Built target hhblits_omp-sse3 make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-sse3.dir/link.d "CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 96%] Built target hhsearch_omp-sse3 make -f src/CMakeFiles/hhalign_omp-sse3.dir/build.make src/CMakeFiles/hhalign_omp-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhalign_omp-sse3.dir/build.make src/CMakeFiles/hhalign_omp-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-sse3.dir/link.d "CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 98%] Built target hhalign_omp-sse3 make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_ca3m-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse3.dir/link.d "CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [100%] Built target hhblits_ca3m-sse3 [100%] Linking CXX executable cstranslate-sse3 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-sse3.dir/link.d "CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-sse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' [100%] Built target cstranslate-sse3 make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd build_plain && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 4%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 6%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h [ 8%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 9%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 11%] Built target hhviterbialgorithm_and_ss make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h [ 13%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 13%] Built target generated make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 13%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/as.cc /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 17%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 19%] Linking C executable ffindex_apply cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 21%] Linking C executable ffindex_reduce cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 23%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 32%] Linking C executable ffindex_unpack cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 32%] Built target ffindex_unpack make 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/log.cc [ 35%] Linking C executable ffindex_order cd 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cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 37%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/application.cc make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 40%] Linking CXX executable a3m_extract-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-plain.dir/link.txt --verbose=1 [ 41%] Linking CXX static library libCS_OBJECTS.a cd 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-std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-plain.dir/link.d "CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o" -o a3m_extract-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/depend make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_reduce-plain.dir/DependInfo.cmake "--color=" [ 41%] Built target a3m_extract-plain make 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/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 44%] Linking CXX executable a3m_reduce-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-plain.dir/link.txt --verbose=1 [ 45%] Linking CXX executable a3m_database_reduce-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-plain.dir/link.d "CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o" -o a3m_reduce-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 45%] Built target a3m_reduce-plain make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-plain.dir/link.d "CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 46%] Built target a3m_database_reduce-plain make -f src/CMakeFiles/a3m_database_filter-plain.dir/build.make src/CMakeFiles/a3m_database_filter-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src 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-ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 48%] Linking CXX executable a3m_database_extract-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-plain.dir/link.d "CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 48%] Built target a3m_database_extract-plain make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP 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-fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection 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-I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated 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directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 90%] Built target hhalign-plain make -f src/CMakeFiles/cstranslate-plain.dir/build.make src/CMakeFiles/cstranslate-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/cstranslate-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/cstranslate-plain.dir/build.make src/CMakeFiles/cstranslate-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 91%] Building CXX object src/CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-plain.dir/link.d "CMakeFiles/hhconsensus-plain.dir/hhconsensus.cpp.o" -o hhconsensus-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 92%] Built target hhconsensus-plain make -f src/CMakeFiles/hhblits_omp-plain.dir/build.make src/CMakeFiles/hhblits_omp-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhblits_omp-plain.dir/build.make src/CMakeFiles/hhblits_omp-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable hhblits_omp-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-plain.dir/link.d "CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o" -o hhblits_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 94%] Built target hhblits_omp-plain make -f src/CMakeFiles/hhsearch_omp-plain.dir/build.make src/CMakeFiles/hhsearch_omp-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhsearch_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhsearch_omp-plain.dir/build.make src/CMakeFiles/hhsearch_omp-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable hhsearch_omp-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-plain.dir/link.d "CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o" -o hhsearch_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 96%] Built target hhsearch_omp-plain make -f src/CMakeFiles/hhalign_omp-plain.dir/build.make src/CMakeFiles/hhalign_omp-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhalign_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhalign_omp-plain.dir/build.make src/CMakeFiles/hhalign_omp-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable hhalign_omp-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-plain.dir/link.d "CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o" -o hhalign_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 98%] Built target hhalign_omp-plain make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_ca3m-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-r2mgi3/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/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void OutputFFIndex::close()’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-plain.dir/link.d "CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [100%] Built target hhblits_ca3m-plain [100%] Linking CXX executable cstranslate-plain cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-plain.dir/link.d "CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o" -o cstranslate-plain libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' [100%] Built target cstranslate-plain make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data cd mybuild/data && make -j2 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' [ 33%] Generating ../generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 66%] Generating ../generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp [100%] Generating ../generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' rm -Rf /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/testdir mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/testdir cd build_plain/src && \ for file in *-plain ; \ do ln -s /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/src/${file} /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/testdir/${file%%-plain} ; done cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/:/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/testdir ./test.sh - 04:08:14.576 INFO: query.a3m is in A2M, A3M or FASTA format - 04:08:15.109 INFO: Alternative alignment: 0 - 04:08:15.115 INFO: 1 alignments done - 04:08:15.132 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 4.29221 Searched_HMMs 1 Date Tue Jan 21 04:08:15 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 529 0 query.a3m 0 32666 3 0 query.a3m 0 32666 73 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 04:08:16.396 INFO: Searching 1 column state sequences. - 04:08:16.444 INFO: query.a3m is in A2M, A3M or FASTA format - 04:08:16.459 INFO: Iteration 1 - 04:08:16.906 INFO: Prefiltering database - 04:08:17.408 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 04:08:17.410 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 04:08:17.410 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 04:08:17.410 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 04:08:17.459 INFO: Alternative alignment: 0 - 04:08:17.466 INFO: 1 alignments done - 04:08:17.466 INFO: Alternative alignment: 1 - 04:08:17.477 INFO: 1 alignments done - 04:08:17.477 INFO: Alternative alignment: 2 - 04:08:17.477 INFO: Alternative alignment: 3 - 04:08:17.959 INFO: Premerge done - 04:08:17.959 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 04:08:17.982 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 4.2743 Searched_HMMs 1 Date Tue Jan 21 04:08:17 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) - 04:08:17.000 INFO: Searching 1 column state sequences. - 04:08:18.073 INFO: Thread 0 query.a3m - 04:08:18.094 INFO: query.a3m is in A2M, A3M or FASTA format - 04:08:18.109 INFO: Iteration 1 - 04:08:18.734 INFO: Prefiltering database - 04:08:19.431 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 04:08:19.431 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 04:08:19.431 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 04:08:19.431 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 04:08:19.454 INFO: Alternative alignment: 0 - 04:08:19.459 INFO: 1 alignments done - 04:08:19.459 INFO: Alternative alignment: 1 - 04:08:19.465 INFO: 1 alignments done - 04:08:19.465 INFO: Alternative alignment: 2 - 04:08:19.465 INFO: Alternative alignment: 3 - 04:08:20.134 INFO: Premerge done - 04:08:20.134 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 04:08:20.153 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 04:08:20.230 INFO: query.a3m is in A2M, A3M or FASTA format - 04:08:20.247 INFO: Searching 1 database HHMs without prefiltering - 04:08:20.247 INFO: Iteration 1 - 04:08:20.816 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 04:08:20.866 INFO: Alternative alignment: 0 - 04:08:20.873 INFO: 1 alignments done - 04:08:20.873 INFO: Alternative alignment: 1 - 04:08:20.882 INFO: 1 alignments done - 04:08:20.883 INFO: Alternative alignment: 2 - 04:08:20.883 INFO: Alternative alignment: 3 - 04:08:21.422 INFO: Premerge done - 04:08:21.423 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 04:08:21.448 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 4.29221 Searched_HMMs 1 Date Tue Jan 21 04:08:21 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) - 04:08:21.541 INFO: Thread 0 query.a3m - 04:08:21.559 INFO: query.a3m is in A2M, A3M or FASTA format - 04:08:21.574 INFO: Searching 1 database HHMs without prefiltering - 04:08:21.574 INFO: Iteration 1 - 04:08:22.166 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 04:08:22.191 INFO: Alternative alignment: 0 - 04:08:22.197 INFO: 1 alignments done - 04:08:22.197 INFO: Alternative alignment: 1 - 04:08:22.202 INFO: 1 alignments done - 04:08:22.202 INFO: Alternative alignment: 2 - 04:08:22.202 INFO: Alternative alignment: 3 - 04:08:22.827 INFO: Premerge done - 04:08:22.827 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 04:08:22.845 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_install --builddirectory build_${SIMD} ; \ done cd build_avx2 && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx2 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx2' cd build_avx && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_avx' cd build_sse4.1 && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse4.1 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse4.1 -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse4.1' cd build_ssse3 && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-ssse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-ssse3 -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_ssse3' cd build_sse3 && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse3 -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse3 -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_sse3' cd build_plain && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-plain -- Installing: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-plain -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/build_plain' mkdir -p /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/hhsuite/usr/bin dh_install -phhsuite debian/bin/simd-dispatch /usr/libexec/hhsuite/ 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 cstranslate ; do dh_install usr/bin/${prog}* /usr/libexec/hhsuite/; done cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/hhsuite/usr/bin \ && 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 \ ln -s ../libexec/hhsuite/simd-dispatch ${prog} ; done cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin \ && for prog in cstranslate ; do \ ln -s ../simd-dispatch ${prog} ; done dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j2 install DESTDIR=/build/hhsuite-r2mgi3/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds -B/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/hhsuite/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/hhsuite/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/hhsuite/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/hhsuite/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/hhsuite/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/hhsuite/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/hhsuite/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_installman -Nhhsuite dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_fixperms -Nhhsuite dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-2), " make[1]: Leaving directory '/build/hhsuite-r2mgi3/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_amd64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_amd64.deb'. dpkg-genbuildinfo -O../hhsuite_3.3.0+ds-8_amd64.buildinfo dpkg-genchanges -O../hhsuite_3.3.0+ds-8_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-21T04:19:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 21 Jan 2025 04:19:04 +0000 | +------------------------------------------------------------------------------+ hhsuite_3.3.0+ds-8_amd64.changes: --------------------------------- Format: 1.8 Date: Sun, 13 Aug 2023 10:47:11 +0200 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: source all amd64 Version: 3.3.0+ds-8 Distribution: perl-5.40-throwaway 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. 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3.3.0+ds-8 Checksums-Md5: b91affbdd2af3b370976fc58fed3d2aa 1243 hhsuite_3.3.0+ds-8.dsc c9b8c4baaf198c024d9f15d0e5ed4ffa 4402152 hhsuite-data_3.3.0+ds-8_all.deb af59056738a9900f33f9e3eb63f92179 126168384 hhsuite-dbgsym_3.3.0+ds-8_amd64.deb f5193e5b4303a19155e8162246d9bc2c 56321076 hhsuite_3.3.0+ds-8_amd64.deb Checksums-Sha1: a31150dbd4ba5a8fee5393a98a505d34720f5aa2 1243 hhsuite_3.3.0+ds-8.dsc 262e7be5b83dc9c81fc3723d97e7a6f2828ad07f 4402152 hhsuite-data_3.3.0+ds-8_all.deb cbca2248a2c01b38f2824cc54a02197d2dc7f8f3 126168384 hhsuite-dbgsym_3.3.0+ds-8_amd64.deb ad7d4c21b33a525b80a7b6a5b7161de751b71d1d 56321076 hhsuite_3.3.0+ds-8_amd64.deb Checksums-Sha256: 35c9801c38ae7554ad58c3b91d452b398dff6a5b834cb52bae4aa458027f252f 1243 hhsuite_3.3.0+ds-8.dsc a63b9845bb3133774e061b97e68ea55d257a970f86cf588d8f4f3123558839a5 4402152 hhsuite-data_3.3.0+ds-8_all.deb 879cec42f5fde7eab0a608a15651a8b18d8e7d5c0d8497346501f84874f7c828 126168384 hhsuite-dbgsym_3.3.0+ds-8_amd64.deb ba4c3d633b71fae2a81e2189ab83ccd5bd0fb9d0f126f9c68ea9df4fcaab3af8 56321076 hhsuite_3.3.0+ds-8_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 21 Jan 2025 04:19:02 +0000 Build-Path: /build/hhsuite-r2mgi3/hhsuite-3.3.0+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), cmake (= 3.31.4-2), cmake-data (= 3.31.4-2), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), fontconfig-config (= 2.15.0-2), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), help2man (= 1.49.3), hicolor-icon-theme (= 0.18-1), hostname (= 3.25), imagemagick (= 8:7.1.1.43+dfsg1-1), imagemagick-7-common (= 8:7.1.1.43+dfsg1-1), imagemagick-7.q16 (= 8:7.1.1.43+dfsg1-1), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-1.1), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbinutils (= 2.43.50.20250108-1), libblkid1 (= 2.40.4-1), libbrotli1 (= 1.1.0-2+b6), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcc1-0 (= 14.2.0-14), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcurl4t64 (= 8.11.1-1+b1), libdav1d7 (= 1.5.0-1+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libde265-0 (= 1.0.15-1+b2), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdeflate0 (= 1.23-1+b1), libdpkg-perl (= 1.22.14), libelf1t64 (= 0.192-4), libexpat1 (= 2.6.4-1), libffi8 (= 3.4.6-1), libfftw3-double3 (= 3.3.10-2+b1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfontconfig1 (= 2.15.0-2), libfreetype6 (= 2.13.3+dfsg-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libglib2.0-0t64 (= 2.82.4-2), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libheif-plugin-dav1d (= 1.19.5-1), libheif-plugin-libde265 (= 1.19.5-1), libheif1 (= 1.19.5-1), libhogweed6t64 (= 3.10-1+b1), libhwasan0 (= 14.2.0-14), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libjbig0 (= 2.1-6.1+b2), libjpeg62-turbo (= 1:2.1.5-3+b1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), liblcms2-2 (= 2.16-2), libldap2 (= 2.6.9+dfsg-1), liblerc4 (= 4.0.0+ds-5), liblocale-gettext-perl (= 1.07-7+b1), liblqr-1-0 (= 0.4.2-2.1+b2), liblsan0 (= 14.2.0-14), libltdl7 (= 2.5.4-2), liblz4-1 (= 1.9.4-4), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmagickcore-7.q16-10 (= 8:7.1.1.43+dfsg1-1), libmagickwand-7.q16-10 (= 8:7.1.1.43+dfsg1-1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libncursesw6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libopenjp2-7 (= 2.5.0-2+b4), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), libpipeline1 (= 1.5.8-1), libpng16-16t64 (= 1.6.45-1), libproc2-0 (= 2:4.0.4-6), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 14.2.0-14), libraw23t64 (= 0.21.3-1+b1), librhash1 (= 1.4.5-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsframe1 (= 2.43.50.20250108-1), libsharpyuv0 (= 1.5.0-0.1), libsimde-dev (= 0.8.2-2), libsmartcols1 (= 2.40.4-1), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsystemd0 (= 257.2-2), libtasn1-6 (= 4.19.0-3+b3), libtiff6 (= 4.5.1+git230720-5), libtinfo6 (= 6.5-2+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.2-2), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libuv1t64 (= 1.48.0-7), libwebp7 (= 1.5.0-0.1), libwebpdemux2 (= 1.5.0-0.1), libwebpmux3 (= 1.5.0-0.1), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b3), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxxhash0 (= 0.8.3-2), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), openssl-provider-legacy (= 3.4.0-2), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), util-linux (= 2.40.4-1), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1691916431" +------------------------------------------------------------------------------+ | Package contents Tue, 21 Jan 2025 04:19:05 +0000 | +------------------------------------------------------------------------------+ hhsuite-data_3.3.0+ds-8_all.deb ------------------------------- new Debian package, version 2.0. size 4402152 bytes: control archive=796 bytes. 593 bytes, 15 lines control 367 bytes, 5 lines md5sums Package: hhsuite-data Source: hhsuite Version: 3.3.0+ds-8 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 12890 Section: science Priority: optional Multi-Arch: foreign Homepage: https://toolkit.tuebingen.mpg.de/ Description: sensitive protein sequence searching based on HMM-HMM alignment (data) HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). . This package contains architecture independent scripts and data files. drwxr-xr-x root/root 0 2023-08-13 08:47 ./ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/data/ lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/data/context_data.crf -> ../../../share/hhsuite/data/context_data.crf lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/data/context_data.lib -> ../../../share/hhsuite/data/context_data.lib lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/data/cs219.lib -> ../../../share/hhsuite/data/cs219.lib drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/hhsuite-data/ -rw-r--r-- root/root 1841 2023-08-13 08:47 ./usr/share/doc/hhsuite-data/changelog.Debian.gz -rw-r--r-- root/root 20399 2023-08-13 08:47 ./usr/share/doc/hhsuite-data/copyright drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/hhsuite/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/hhsuite/data/ -rw-r--r-- root/root 7186806 2020-08-16 23:16 ./usr/share/hhsuite/data/context_data.crf -rw-r--r-- root/root 5922161 2020-08-16 23:16 ./usr/share/hhsuite/data/context_data.lib -rw-r--r-- root/root 51634 2020-08-16 23:16 ./usr/share/hhsuite/data/cs219.lib hhsuite-dbgsym_3.3.0+ds-8_amd64.deb ----------------------------------- new Debian package, version 2.0. size 126168384 bytes: control archive=5184 bytes. 4643 bytes, 12 lines control 11214 bytes, 106 lines md5sums Package: hhsuite-dbgsym Source: hhsuite Version: 3.3.0+ds-8 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 550064 Depends: hhsuite (= 3.3.0+ds-8) Section: debug Priority: optional Description: debug symbols for hhsuite Build-Ids: 02f86492dc82a68433d09c55f2eb5172170fffd6 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hhsuite hhsuite_3.3.0+ds-8_amd64.deb ---------------------------- new Debian package, version 2.0. size 56321076 bytes: control archive=4596 bytes. 1472 bytes, 29 lines control 10398 bytes, 146 lines md5sums Package: hhsuite Version: 3.3.0+ds-8 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 467535 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 14), perl:any, hhsuite-data (= 3.3.0+ds-8), python3 Conflicts: ffindex Built-Using: simde (= 0.8.2-2) Section: science Priority: optional Homepage: https://toolkit.tuebingen.mpg.de/ Description: sensitive protein sequence searching based on HMM-HMM alignment HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). . This package contains HHsearch and HHblits among other programs and utilities. . HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling. . HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. drwxr-xr-x root/root 0 2023-08-13 08:47 ./ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/bin/ lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/a3m_database_extract -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/a3m_database_filter -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/a3m_database_reduce -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/a3m_extract -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/a3m_reduce -> ../libexec/hhsuite/simd-dispatch -rwxr-xr-x root/root 31136 2023-08-13 08:47 ./usr/bin/ffindex_apply -rwxr-xr-x root/root 31200 2023-08-13 08:47 ./usr/bin/ffindex_build -rwxr-xr-x root/root 26976 2023-08-13 08:47 ./usr/bin/ffindex_from_fasta -rwxr-xr-x root/root 30960 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0 2023-08-13 08:47 ./usr/bin/hhfilter -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/hhmake -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/hhsearch -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/bin/hhsearch_omp -> ../libexec/hhsuite/simd-dispatch drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/ lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hh -> hhsuite drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/data/ -rw-r--r-- root/root 1986 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete -rw-r--r-- root/root 135 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.phr -rw-r--r-- root/root 112 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.pin -rw-r--r-- root/root 433 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.psq lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/hhsuite/ -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-avx -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-avx2 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-plain -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-sse3 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-sse4.1 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_extract-ssse3 -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-avx -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-avx2 -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-plain -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-sse3 -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-sse4.1 -rwxr-xr-x root/root 59800 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_filter-ssse3 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-avx -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-avx2 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-plain -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-sse3 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-sse4.1 -rwxr-xr-x root/root 51608 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_database_reduce-ssse3 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-avx -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-avx2 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-plain -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-sse3 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-sse4.1 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_extract-ssse3 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-avx -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-avx2 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-plain -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-sse3 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-sse4.1 -rwxr-xr-x root/root 47432 2023-08-13 08:47 ./usr/libexec/hhsuite/a3m_reduce-ssse3 drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/hhsuite/bin/ lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/libexec/hhsuite/bin/cstranslate -> ../simd-dispatch -rwxr-xr-x root/root 6261224 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-avx -rwxr-xr-x root/root 6261224 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-avx2 -rwxr-xr-x root/root 6257128 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-plain -rwxr-xr-x root/root 6257128 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-sse3 -rwxr-xr-x root/root 6257128 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-sse4.1 -rwxr-xr-x root/root 6257128 2023-08-13 08:47 ./usr/libexec/hhsuite/cstranslate-ssse3 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-avx -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-avx2 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-plain -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-sse3 -rwxr-xr-x root/root 8227240 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-sse4.1 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign-ssse3 -rwxr-xr-x root/root 8243624 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-avx -rwxr-xr-x root/root 8235432 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-avx2 -rwxr-xr-x root/root 8239528 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-plain -rwxr-xr-x root/root 8239528 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-sse3 -rwxr-xr-x root/root 8235432 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-sse4.1 -rwxr-xr-x root/root 8239528 2023-08-13 08:47 ./usr/libexec/hhsuite/hhalign_omp-ssse3 -rwxr-xr-x root/root 8182184 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-avx -rwxr-xr-x root/root 8173992 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-avx2 -rwxr-xr-x root/root 8178088 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-plain -rwxr-xr-x root/root 8178088 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-sse3 -rwxr-xr-x root/root 8178088 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-sse4.1 -rwxr-xr-x root/root 8178088 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits-ssse3 -rwxr-xr-x root/root 8190376 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-avx -rwxr-xr-x root/root 8178088 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-avx2 -rwxr-xr-x root/root 8190376 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-plain -rwxr-xr-x root/root 8190376 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-sse3 -rwxr-xr-x root/root 8186280 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-sse4.1 -rwxr-xr-x root/root 8190376 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_ca3m-ssse3 -rwxr-xr-x root/root 8190376 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-avx -rwxr-xr-x root/root 8182184 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-avx2 -rwxr-xr-x root/root 8186280 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-plain -rwxr-xr-x root/root 8186280 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-sse3 -rwxr-xr-x root/root 8182184 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-sse4.1 -rwxr-xr-x root/root 8186280 2023-08-13 08:47 ./usr/libexec/hhsuite/hhblits_omp-ssse3 -rwxr-xr-x root/root 7645608 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-avx -rwxr-xr-x root/root 7649704 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-avx2 -rwxr-xr-x root/root 7641512 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-plain -rwxr-xr-x root/root 7641512 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-sse3 -rwxr-xr-x root/root 7641512 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-sse4.1 -rwxr-xr-x root/root 7641512 2023-08-13 08:47 ./usr/libexec/hhsuite/hhconsensus-ssse3 -rwxr-xr-x root/root 362912 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-avx -rwxr-xr-x root/root 367008 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-avx2 -rwxr-xr-x root/root 358816 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-plain -rwxr-xr-x root/root 358816 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-sse3 -rwxr-xr-x root/root 358816 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-sse4.1 -rwxr-xr-x root/root 358816 2023-08-13 08:47 ./usr/libexec/hhsuite/hhfilter-ssse3 -rwxr-xr-x root/root 7625128 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-avx -rwxr-xr-x root/root 7625128 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-avx2 -rwxr-xr-x root/root 7616936 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-plain -rwxr-xr-x root/root 7616936 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-sse3 -rwxr-xr-x root/root 7616936 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-sse4.1 -rwxr-xr-x root/root 7616936 2023-08-13 08:47 ./usr/libexec/hhsuite/hhmake-ssse3 -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-avx -rwxr-xr-x root/root 8210856 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-avx2 -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-plain -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-sse3 -rwxr-xr-x root/root 8219048 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-sse4.1 -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch-ssse3 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-avx -rwxr-xr-x root/root 8223144 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-avx2 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-plain -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-sse3 -rwxr-xr-x root/root 8227240 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-sse4.1 -rwxr-xr-x root/root 8231336 2023-08-13 08:47 ./usr/libexec/hhsuite/hhsearch_omp-ssse3 -rwxr-xr-x root/root 453 2023-08-13 08:47 ./usr/libexec/hhsuite/simd-dispatch drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/hhsuite/ -rw-r--r-- root/root 1986 2020-08-16 23:16 ./usr/share/doc/hhsuite/README.md.gz -rw-r--r-- root/root 1841 2023-08-13 08:47 ./usr/share/doc/hhsuite/changelog.Debian.gz -rw-r--r-- root/root 20399 2023-08-13 08:47 ./usr/share/doc/hhsuite/copyright drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/hhsuite/examples/ -rw-r--r-- root/root 32126 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.a3m -rw-r--r-- root/root 57578 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.hhm -rw-r--r-- root/root 181765 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.hhr -rw-r--r-- root/root 506 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.seq drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/hhsuite/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/hhsuite/scripts/ -rw-r--r-- root/root 24577 2020-08-16 23:16 ./usr/share/hhsuite/scripts/Align.pm -rw-r--r-- root/root 4710 2020-08-16 23:16 ./usr/share/hhsuite/scripts/HHPaths.pm -rwxr-xr-x root/root 8021 2023-08-13 08:47 ./usr/share/hhsuite/scripts/a3m.py -rwxr-xr-x root/root 31681 2023-08-13 08:47 ./usr/share/hhsuite/scripts/addss.pl -rwxr-xr-x root/root 438 2023-08-13 08:47 ./usr/share/hhsuite/scripts/check_a3m.py -rwxr-xr-x root/root 28735 2023-08-13 08:47 ./usr/share/hhsuite/scripts/cif2fasta.py -rwxr-xr-x root/root 4654 2023-08-13 08:47 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl -rwxr-xr-x root/root 6815 2023-08-13 08:47 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl -rwxr-xr-x root/root 2081 2023-08-13 08:47 ./usr/share/hhsuite/scripts/ffindex.py -rwxr-xr-x root/root 446 2023-08-13 08:47 ./usr/share/hhsuite/scripts/get_a3m_size.py -rwxr-xr-x root/root 7179 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hh_reader.py -rwxr-xr-x root/root 48079 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hhmakemodel.pl -rwxr-xr-x root/root 87343 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hhmakemodel.py -rwxr-xr-x root/root 16961 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hhsuitedb.py -rwxr-xr-x root/root 20214 2020-08-16 23:16 ./usr/share/hhsuite/scripts/mergeali.pl -rwxr-xr-x root/root 5717 2023-08-13 08:47 ./usr/share/hhsuite/scripts/multithread.pl -rwxr-xr-x root/root 40490 2023-08-13 08:47 ./usr/share/hhsuite/scripts/pdb2fasta.pl -rwxr-xr-x root/root 13183 2023-08-13 08:47 ./usr/share/hhsuite/scripts/pdbfilter.pl -rwxr-xr-x root/root 8648 2023-08-13 08:47 ./usr/share/hhsuite/scripts/pdbfilter.py -rwxr-xr-x root/root 28328 2020-08-16 23:16 ./usr/share/hhsuite/scripts/reformat.pl -rwxr-xr-x root/root 14019 2023-08-13 08:47 ./usr/share/hhsuite/scripts/renumberpdb.pl -rwxr-xr-x root/root 3651 2023-08-13 08:47 ./usr/share/hhsuite/scripts/splitfasta.pl drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/man/ drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/man/man1/ -rw-r--r-- root/root 3088 2023-08-13 08:47 ./usr/share/man/man1/hhalign.1.gz -rw-r--r-- root/root 4141 2023-08-13 08:47 ./usr/share/man/man1/hhblits.1.gz -rw-r--r-- root/root 4151 2023-08-13 08:47 ./usr/share/man/man1/hhblits_omp.1.gz -rw-r--r-- root/root 1029 2023-08-13 08:47 ./usr/share/man/man1/hhconsensus.1.gz -rw-r--r-- root/root 1021 2023-08-13 08:47 ./usr/share/man/man1/hhfilter.1.gz -rw-r--r-- root/root 1656 2023-08-13 08:47 ./usr/share/man/man1/hhmake.1.gz -rw-r--r-- root/root 3357 2023-08-13 08:47 ./usr/share/man/man1/hhsearch.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 21 Jan 2025 04:19:11 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 21 Jan 2025 04:19:11 +0000 | +------------------------------------------------------------------------------+ Purging /build/hhsuite-r2mgi3 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 21 Jan 2025 04:19:12 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 3771544 Build-Time: 1468 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/hhsuite_3.3.0+ds-8.dsc Machine Architecture: amd64 Package: hhsuite Package-Time: 1487 Source-Version: 3.3.0+ds-8 Space: 3771544 Status: successful Version: 3.3.0+ds-8 -------------------------------------------------------------------------------- Finished at 2025-01-21T04:19:04Z Build needed 00:24:47, 3771544k disk space