sbuild (Debian sbuild) 0.90.2 (26 August 2025) on carme.larted.org.uk +==============================================================================+ | hhsuite 3.3.0+ds-9 (amd64) Sat, 18 Oct 2025 00:01:41 +0000 | +==============================================================================+ Package: hhsuite Version: 3.3.0+ds-9 Source Version: 3.3.0+ds-9 Distribution: perl-5.42-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 Sat, 18 Oct 2025 00:01:41 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hhsuite_3.3.0+ds-9 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup hhsuite_3.3.0+ds-9 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 18 Oct 2025 00:01:41 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease 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 Sat, 18 Oct 2025 00:01:43 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/hhsuite_3.3.0+ds-9.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 18 Oct 2025 00:01:44 +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-RuXJna/resolver-V2qAC6/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/apt_archive ./ InRelease Get:2 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/apt_archive ./ Release [609 B] Ign:3 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/apt_archive ./ Release.gpg Get:4 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/apt_archive ./ Sources [644 B] Get:5 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/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 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 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 libxml2-16 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 gnulib-l10n 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 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 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 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 libxml2-16 m4 man-db po-debconf procps sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 40.3 MB/43.4 MB of archives. After this operation, 156 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 liblocale-gettext-perl amd64 1.07-7+b2 [15.3 kB] Get:2 copy:/build/hhsuite-RuXJna/resolver-V2qAC6/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [884 B] Get:3 file:/srv/reprepro perl-5.42/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.2.3+dfsg1-1+b1 [1942 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:7 file:/srv/reprepro perl-5.42/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.2.3+dfsg1-1+b1 [376 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:10 file:/srv/reprepro perl-5.42/main amd64 imagemagick-7.q16 amd64 8:7.1.2.3+dfsg1-1+b1 [728 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:13 file:/srv/reprepro perl-5.42/main amd64 imagemagick amd64 8:7.1.2.3+dfsg1-1+b1 [21.8 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.20.2-2+b1 [19.1 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.16-1 [189 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.20.2-2+b1 [17.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.20.2-2+b1 [601 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.86.0-5 [1544 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libraw23t64 amd64 0.21.4-2 [390 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 imagemagick-7-common all 8:7.1.2.3+dfsg1-1 [69.0 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:69 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-4 [408 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:87 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Preconfiguring packages ... Fetched 40.3 MB in 0s (131 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 23301 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../01-libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../02-libfftw3-double3_3.3.10-2+b1_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../03-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../04-libpng16-16t64_1.6.50-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.50-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../05-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../08-fontconfig-config_2.15.0-2.4_amd64.deb ... Unpacking fontconfig-config (2.15.0-2.4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../09-libfontconfig1_2.15.0-2.4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2.4) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../10-libsharpyuv0_1.5.0-0.1_amd64.deb ... 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Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up cmake-data (4.1.1+really3.31.6-2) ... Setting up librhash1:amd64 (1.4.6-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libde265-0:amd64 (1.0.16-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up liblocale-gettext-perl (1.07-7+b2) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... 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 (21) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.16.0-1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libcurl4t64:amd64 (8.16.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (4.1.1+really3.31.6-2) ... Setting up debhelper (13.28) ... Setting up libheif-plugin-dav1d:amd64 (1.20.2-2+b1) ... Setting up libheif1:amd64 (1.20.2-2+b1) ... Setting up libmagickcore-7.q16-10:amd64 (8:7.1.2.3+dfsg1-1+b1) ... Setting up libheif-plugin-libde265:amd64 (1.20.2-2+b1) ... Setting up libmagickwand-7.q16-10:amd64 (8:7.1.2.3+dfsg1-1+b1) ... Setting up imagemagick-7.q16 (8:7.1.2.3+dfsg1-1+b1) ... 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: 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 (magick) in auto mode 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 (8:7.1.2.3+dfsg1-1+b1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sat, 18 Oct 2025 00:01:53 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sat, 18 Oct 2025 00:01:53 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.16.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.16.5-1 (2025-09-05) amd64 (x86_64) Toolchain package versions: binutils_2.45-7 dpkg-dev_1.22.21 g++-14_14.3.0-8 g++-15_15.2.0-4 gcc-14_14.3.0-8 gcc-15_15.2.0-4 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-8 libstdc++-15-dev_15.2.0-4 libstdc++6_15.2.0-4 linux-libc-dev_6.16.12-2 Package versions: adduser_3.153 apt_3.1.8 autoconf_2.72-3.1 automake_1:1.18.1-2 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.3-1 binutils_2.45-7 binutils-common_2.45-7 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.45-7 bsdextrautils_2.41.2-4 bsdutils_1:2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 cmake_4.1.1+really3.31.6-2 cmake-data_4.1.1+really3.31.6-2 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-14_14.3.0-8 cpp-14-x86-64-linux-gnu_14.3.0-8 cpp-15_15.2.0-4 cpp-15-x86-64-linux-gnu_15.2.0-4 cpp-x86-64-linux-gnu_4:15.2.0-4 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.10-4 dirmngr_2.4.8-3 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 fontconfig-config_2.15.0-2.4 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:15.2.0-4 g++-14_14.3.0-8 g++-14-x86-64-linux-gnu_14.3.0-8 g++-15_15.2.0-4 g++-15-x86-64-linux-gnu_15.2.0-4 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-14_14.3.0-8 gcc-14-base_14.3.0-8 gcc-14-x86-64-linux-gnu_14.3.0-8 gcc-15_15.2.0-4 gcc-15-base_15.2.0-4 gcc-15-x86-64-linux-gnu_15.2.0-4 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-3 gnupg-l10n_2.4.8-3 gpg_2.4.8-3 gpg-agent_2.4.8-3 gpgconf_2.4.8-3 gpgsm_2.4.8-3 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 help2man_1.49.3 hicolor-icon-theme_0.18-2 hostname_3.25 imagemagick_8:7.1.2.3+dfsg1-1+b1 imagemagick-7-common_8:7.1.2.3+dfsg1-1 imagemagick-7.q16_8:7.1.2.3+dfsg1-1+b1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.8 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-4+b1 libasan8_15.2.0-4 libassuan9_3.0.2-2 libatomic1_15.2.0-4 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbinutils_2.45-7 libblkid1_2.41.2-4 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc-l10n_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-4 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-7 libctf0_2.45-7 libcurl4t64_8.16.0-4 libdav1d7_1.5.1-1 libdb5.3t64_5.3.28+dfsg2-10 libde265-0_1.0.16-1 libdebconfclient0_0.280 libdebhelper-perl_13.28 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.193-3 libexpat1_2.7.3-1 libffi8_3.5.2-2 libfftw3-double3_3.3.10-2+b1 libfile-stripnondeterminism-perl_1.15.0-1 libfontconfig1_2.15.0-2.4 libfreetype6_2.13.3+dfsg-1 libgcc-14-dev_14.3.0-8 libgcc-15-dev_15.2.0-4 libgcc-s1_15.2.0-4 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libglib2.0-0t64_2.86.0-5 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-4 libgpg-error0_1.56-2 libgprofng0_2.45-7 libgssapi-krb5-2_1.21.3-5 libheif-plugin-dav1d_1.20.2-2+b1 libheif-plugin-libde265_1.20.2-2+b1 libheif1_1.20.2-2+b1 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-4 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-4 libjansson4_2.14-2+b3 libjbig0_2.1-6.1+b2 libjpeg62-turbo_1:2.1.5-4 libjsoncpp26_1.9.6-4 libk5crypto3_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.2-4 liblcms2-2_2.16-2 libldap2_2.6.10+dfsg-1+b1 liblerc4_4.0.0+ds-5 liblocale-gettext-perl_1.07-7+b2 liblqr-1-0_0.4.2-2.1+b2 liblsan0_15.2.0-4 libltdl7_2.5.4-5 liblz4-1_1.10.0-4 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmagickcore-7.q16-10_8:7.1.2.3+dfsg1-1+b1 libmagickwand-7.q16-10_8:7.1.2.3+dfsg1-1+b1 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-ossl0_1.16.0-1 libnpth0t64_1.8-3 libopenjp2-7_2.5.3-2.1 libp11-kit0_0.25.9-2 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-2 libpipeline1_1.5.8-1 libpng16-16t64_1.6.50-1 libproc2-0_2:4.0.4-9 libpsl5t64_0.21.2-1.1+b1 libquadmath0_15.2.0-4 libraw23t64_0.21.4-2 libreadline8t64_8.3-3 librhash1_1.4.6-1 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.9-2 libsframe2_2.45-7 libsharpyuv0_1.5.0-0.1 libsimde-dev_0.8.2-3 libsmartcols1_2.41.2-4 libsqlite3-0_3.46.1-8 libssh2-1t64_1.11.1-1 libssl3t64_3.5.4-1 libstdc++-14-dev_14.3.0-8 libstdc++-15-dev_15.2.0-4 libstdc++6_15.2.0-4 libsystemd0_258.1-1 libtasn1-6_4.20.0-2 libtiff6_4.7.1-1 libtinfo6_6.5+20250216-2 libtool_2.5.4-5 libtsan2_15.2.0-4 libubsan1_15.2.0-4 libuchardet0_0.0.8-2 libudev1_258.1-1 libunistring5_1.3-2 libuuid1_2.41.2-4 libuv1t64_1.51.0-2 libwebp7_1.5.0-0.1 libwebpdemux2_1.5.0-0.1 libwebpmux3_1.5.0-0.1 libx11-6_2:1.8.12-1 libx11-data_2:1.8.12-1 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 libxml2-16_2.14.6+dfsg-0.1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.16.12-2 locales-all_2.41-12 login.defs_1:4.18.0-1 m4_1.4.20-2 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.4-1 passwd_1:4.18.0-1 patch_2.8-2 perl_5.42.0-2 perl-base_5.42.0-2 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-2 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 procps_2:4.0.4-9 readline-common_8.3-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.2-4 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sat, 18 Oct 2025 00:01:53 +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-9 Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille , Sascha Steinbiss , Homepage: https://toolkit.tuebingen.mpg.de/ Standards-Version: 4.7.2 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 128e4d8b43032a85c68321b4a4661e17c1f23044 16904 hhsuite_3.3.0+ds-9.debian.tar.xz Checksums-Sha256: a81037f2e2a4801f1a42f5aa5939334fe038053d05ceabdc0899fefb8cc00a44 4775072 hhsuite_3.3.0+ds.orig.tar.xz 930c7195042d4c83975b99039a4df4904041a557a8d142f38dcc94f4ecc3f900 16904 hhsuite_3.3.0+ds-9.debian.tar.xz Files: d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz 4bb89a0a1a1f74616d3a20353441f119 16904 hhsuite_3.3.0+ds-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmjyZMkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGUng/8DARYxNCdXH2u7niHsiA+3O/aP9vlylHN nHOhDi1BU+CDGNYwKls9rRqbY2vsPqe/JagvsbBqLDOqY62TC0j7/pY+5MK8ZdcB PumSfXSbbaA4FsOOxjlInYXa1HrXO9n+NtfAXuFQ9GGZmxRtVEytKcVZ3XDF5lA7 6YpsPCuBR9cMclyE0bfLEwM5ALZJKi4w4KSB90oRQOOPfti1TQSc3GKz+ydAqxdc MmC+Uhe2mF/TYidVBRtm8bd2FBEVgYuhIr/at5kwgb7UOrdempVKG3ewvTmkdCWW JtIc/XkO1bHDmY2DSv2gN+7EHGsWwdquQu3m/Lc1sMKv6/qaFULSZm2Ja4NtWD6y iMtJgD/Js467eN6uDOBCNasJg+3fSHRNtkWXcYa1WEKm4UYHYhBYC1jKGKjwR5wG KcT/sTWAWPZTB9Q3fa7xbCz57w5V1z7PhjdqXIHsYqn119zh0bR/KmRJpQiRbQFK C4zPbBH20wqD5T+/wOVUYooYDU1YHiKBXTiK3VXJz/qPLHP+XyIUwam1mR+s+pPf Bs4RMJ4g8YIZSyxWtBRCkwLPAdn9sxBfqVUufE/7o7be8q/R1vWKZT13nIHtV4AS /q4P0CJZbSVihhlvKrFnZi2xhkwmzws3uVViq3DSnsdXKMwyhLvFEIQ2k0hetwJu TpJWe3iaTro= =Uxj1 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-9.dsc: no acceptable signature found dpkg-source: info: extracting hhsuite in /build/hhsuite-RuXJna/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-9.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 Sat, 18 Oct 2025 00:01:53 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hhsuite_3.3.0+ds-9 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network hhsuite_3.3.0+ds-9 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-RuXJna/hhsuite-3.3.0+ds SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-097f7e66-8ddd-4bb3-941c-7164c3ba5e7a 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-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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-RuXJna/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-RuXJna/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-9.debian.tar.xz dpkg-source: info: building hhsuite in hhsuite_3.3.0+ds-9.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-RuXJna/hhsuite-3.3.0+ds' for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ; \ 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 (2.1s) -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 (2.1s) -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 (1.6s) -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 (1.6s) -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain make[1]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 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 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 (1.6s) -- 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild make[1]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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 -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h [ 6%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h [ 7%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h [ 9%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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_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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 16%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 16%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 18%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 20%] Built target ffindex_apply [ 21%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/log.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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 22%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 23%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 23%] Built target ffindex_reduce [ 24%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 26%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 26%] Built target ffindex_build make -f 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lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 28%] Linking C executable ffindex_from_fasta cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 30%] Linking C executable ffindex_get cd /build/hhsuite-RuXJna/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 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 32%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 34%] Linking C executable ffindex_unpack cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_order cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' 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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 38%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -P 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-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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 39%] Built target CS_OBJECTS make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/depend [ 39%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_extract-avx2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_reduce-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/build [ 40%] Building CXX object src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 41%] Building CXX object src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 42%] Linking CXX executable a3m_extract-avx2 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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_extract-avx2.dir/link.d "CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o" -o a3m_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 42%] Built target a3m_extract-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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_reduce-avx2.dir/DependInfo.cmake "--color=" [ 43%] Linking CXX executable a3m_reduce-avx2 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 44%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 44%] Built target a3m_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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_extract-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 45%] Building CXX object src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 46%] Linking CXX executable a3m_database_reduce-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 46%] Built target a3m_database_reduce-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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_filter-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 47%] Building CXX object src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 48%] Linking CXX executable a3m_database_extract-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 48%] Built target a3m_database_extract-avx2 make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.cpp [ 50%] Linking CXX executable a3m_database_filter-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 50%] Built target a3m_database_filter-avx2 [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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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/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-RuXJna/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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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits-avx2.dir/build.make src/CMakeFiles/hhblits-avx2.dir/depend make -f src/CMakeFiles/hhmake-avx2.dir/build.make src/CMakeFiles/hhmake-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits-avx2.dir/DependInfo.cmake "--color=" cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhmake-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits-avx2.dir/build.make src/CMakeFiles/hhblits-avx2.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 80%] Building CXX object src/CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-avx2.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhmake-avx2.dir/build.make 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src/CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhmake.cpp [ 82%] Linking CXX executable hhblits-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 82%] Built target hhblits-avx2 make -f src/CMakeFiles/hhfilter-avx2.dir/build.make src/CMakeFiles/hhfilter-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhfilter-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhfilter-avx2.dir/build.make src/CMakeFiles/hhfilter-avx2.dir/build make[4]: Entering directory 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CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-avx2 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhmake-avx2.dir/link.d "CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o" -o hhmake-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a 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object src/CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-avx2.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o.d -o 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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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 88%] Built target hhsearch-avx2 make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhconsensus-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && 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/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 90%] Built target hhalign-avx2 make -f src/CMakeFiles/cstranslate-avx2.dir/build.make 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhsearch_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhalign_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_ca3m-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp [ 99%] Linking CXX executable cstranslate-avx2 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [ 99%] Built target cstranslate-avx2 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx2' [100%] Built target hhblits_ca3m-avx2 make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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 -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 1%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 4%] Built target ffindex [ 5%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h [ 6%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/cs219.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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 9%] 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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 /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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 15%] Built target hhviterbialgorithm_and_ss [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 16%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/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-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 18%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/log.cc [ 23%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 23%] 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 25%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 25%] Built target ffindex_build [ 26%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 28%] Linking C executable ffindex_from_fasta cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 30%] Linking C executable ffindex_get cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' 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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 32%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' 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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 34%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 [ 35%] Linking C executable ffindex_unpack cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.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 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lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 37%] Linking C executable ffindex_order [ 38%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 40%] Built target ffindex_from_fasta_with_split [ 41%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 42%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp [ 43%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 44%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 45%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 46%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/util.cpp [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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 ()); | ~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_extract-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 55%] Building CXX object src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 56%] Linking CXX executable a3m_extract-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 56%] Built target a3m_extract-avx make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_reduce-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 57%] Building CXX object src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 58%] Linking CXX executable a3m_reduce-avx cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 58%] Built target a3m_reduce-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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_reduce-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 59%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 61%] Linking CXX executable a3m_database_reduce-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 61%] Built target a3m_database_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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_extract-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 62%] Building CXX object src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 63%] Linking CXX executable a3m_database_extract-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 63%] Built target a3m_database_extract-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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_filter-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 64%] Building CXX object src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 66%] Linking CXX executable a3m_database_filter-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 66%] Built target a3m_database_filter-avx [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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 CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhmake-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhmake-avx.dir/build.make src/CMakeFiles/hhmake-avx.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 80%] Building CXX object src/CMakeFiles/hhmake-avx.dir/hhmake.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhmake-avx.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-avx.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-avx.dir/hhmake.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhmake.cpp make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits-avx.dir/build.make src/CMakeFiles/hhblits-avx.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 81%] Building CXX object src/CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 82%] Linking CXX executable hhblits-avx cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx.dir/link.txt --verbose=1 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-avx cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 86%] Linking CXX executable hhsearch-avx cd /build/hhsuite-RuXJna/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 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script 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-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-avx.dir/link.d "CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o" -o 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 [ 87%] Built target hhfilter-avx make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhalign-avx.dir/build.make src/CMakeFiles/hhalign-avx.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx 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'/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 88%] Building CXX object src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 89%] Building CXX object src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/cstranslate-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 91%] Building CXX object src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-avx cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhsearch_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_ca3m-avx.dir/DependInfo.cmake "--color=" [ 98%] Linking CXX executable cstranslate-avx cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [ 99%] Built target cstranslate-avx /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_avx' [100%] Built target hhblits_ca3m-avx make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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 make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h [ 8%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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 /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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h [ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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 [ 12%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h [ 12%] Built target hhviterbialgorithm_and_ss make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/aa.cc [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 13%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/as.cc [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 16%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 16%] 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 17%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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 [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 19%] Linking C executable ffindex_apply cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 21%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 21%] 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 22%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 23%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 23%] Built target ffindex_build [ 24%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 25%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs/log.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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 27%] Linking C executable ffindex_from_fasta cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 27%] Built target ffindex_from_fasta [ 28%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 30%] Linking C executable ffindex_get cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/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 [ 33%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-RuXJna/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-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' /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 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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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 36%] Linking C executable ffindex_order cd /build/hhsuite-RuXJna/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/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 36%] Built target ffindex_order make -f 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Linking C executable ffindex_unpack cd /build/hhsuite-RuXJna/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 [ 38%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 38%] Built target ffindex_unpack make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 39%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.cpp [ 40%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_extract-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_extract-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 41%] Building CXX object src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 42%] Linking CXX executable a3m_extract-sse4.1 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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_extract-sse4.1.dir/link.d "CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o" -o a3m_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 42%] Built target a3m_extract-sse4.1 make -f src/CMakeFiles/a3m_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_reduce-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_reduce-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_reduce-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 43%] Building CXX object src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 44%] Linking CXX executable a3m_reduce-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 44%] Built target a3m_reduce-sse4.1 make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_database_reduce-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 45%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 46%] Linking CXX executable a3m_database_reduce-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 46%] 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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_database_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_database_extract-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 47%] Building CXX object src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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_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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 48%] Linking CXX executable a3m_database_extract-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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_extract-sse4.1.dir/link.d "CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 48%] Built target a3m_database_extract-sse4.1 [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd 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52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.cpp make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_database_filter-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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 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-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 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 55%] Linking CXX executable a3m_database_filter-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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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-ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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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CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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-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/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/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 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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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make 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libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhconsensus-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhconsensus-sse4.1.dir/build.make src/CMakeFiles/hhconsensus-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/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-RuXJna/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/cstranslate-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-sse4.1 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_ca3m-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' [100%] Built target cstranslate-sse4.1 make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 4%] Built target ffindex [ 5%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp [ 6%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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 [ 10%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake /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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 [ 10%] 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" /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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 10%] Built target hhviterbialgorithm_with_celloff make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/aa.cc make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 12%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 15%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 18%] Built target A3M_COMPRESS [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/log.cc [ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/application.cc make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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 [ 22%] Linking C executable ffindex_apply cd /build/hhsuite-RuXJna/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 [ 23%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' /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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 23%] 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" [ 23%] Built target CS_OBJECTS make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 26%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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 [ 27%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/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-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 32%] Linking C executable ffindex_from_fasta [ 33%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/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 cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 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-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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 33%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/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 make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_unpack cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 37%] Linking C executable ffindex_order cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" cd /build/hhsuite-RuXJna/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 make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 38%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" [ 39%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-RuXJna/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 make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 40%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits.cpp /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 40%] 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_extract-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 41%] Building CXX object src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 42%] Linking CXX executable a3m_extract-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 42%] Built target a3m_extract-ssse3 make -f src/CMakeFiles/a3m_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_reduce-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_reduce-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_reduce-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 43%] Building CXX object src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 44%] Linking CXX executable a3m_reduce-ssse3 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script 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-E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_reduce-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 45%] Building CXX object src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 46%] Linking CXX executable a3m_database_reduce-ssse3 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp 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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_extract-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 49%] Building CXX object src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 50%] Linking CXX executable a3m_database_extract-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 50%] Built target a3m_database_extract-ssse3 [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmatrices.cpp make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_filter-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 52%] Building CXX object src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 53%] Linking CXX executable a3m_database_filter-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 53%] Built target a3m_database_filter-ssse3 [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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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/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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 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[ 84%] Linking CXX executable hhmake-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 84%] Built target hhmake-ssse3 make -f 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-ssse3.dir/link.txt --verbose=1 [ 87%] Linking CXX executable hhfilter-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 87%] Built target hhsearch-ssse3 make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhalign-ssse3.dir/DependInfo.cmake "--color=" [ 87%] Built target hhfilter-ssse3 make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhconsensus-ssse3.dir/DependInfo.cmake "--color=" [ 88%] Building CXX object src/CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/cstranslate-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 91%] Building CXX object src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhsearch_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhalign_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_ca3m-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-ssse3.dir/link.txt --verbose=1 [100%] Linking CXX executable cstranslate-ssse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target hhblits_ca3m-ssse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target cstranslate-ssse3 make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' 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 make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 4%] Built target ffindex [ 5%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h [ 6%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/cs219.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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 9%] 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/as.cc [ 14%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 26%] Linking C executable ffindex_from_fasta cd /build/hhsuite-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 28%] Linking C executable ffindex_get cd /build/hhsuite-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 30%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/log.cc [ 31%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 31%] 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd 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/build/hhsuite-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 33%] Built target ffindex_unpack [ 34%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/application.cc 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_order cd /build/hhsuite-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 38%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_extract-sse3.dir/build.make src/CMakeFiles/a3m_extract-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_extract-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 39%] Building CXX object src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 40%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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 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'/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 41%] Building CXX object src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 42%] Linking CXX executable a3m_extract-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 42%] Built target a3m_extract-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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_reduce-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 44%] Linking CXX executable a3m_reduce-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 44%] Built target a3m_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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_extract-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 45%] Building CXX object src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 46%] Linking CXX executable a3m_database_reduce-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 46%] Built target a3m_database_reduce-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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_filter-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_filter-sse3.dir/build.make src/CMakeFiles/a3m_database_filter-sse3.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 47%] Building CXX object src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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-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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 48%] Built target a3m_database_extract-sse3 make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 50%] Built target a3m_database_filter-sse3 [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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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/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated 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CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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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/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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 CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits-sse3.dir/build.make src/CMakeFiles/hhblits-sse3.dir/depend make -f src/CMakeFiles/hhmake-sse3.dir/build.make src/CMakeFiles/hhmake-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src 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'/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 80%] Building CXX object src/CMakeFiles/hhblits-sse3.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-sse3.dir/hhblits_app.cpp.o -MF 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libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhfilter-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhfilter-sse3.dir/build.make src/CMakeFiles/hhfilter-sse3.dir/build make[4]: Entering directory 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CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Linking CXX executable hhmake-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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 '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 85%] Building CXX object src/CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-sse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o.d -o 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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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_app.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhconsensus-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 89%] Building CXX object src/CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 90%] Linking CXX executable hhalign-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/cstranslate-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 91%] Building CXX object src/CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_ca3m-sse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse3.dir/link.txt --verbose=1 [100%] Linking CXX executable cstranslate-sse3 cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [100%] Built target cstranslate-sse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_sse3' [100%] Built target hhblits_ca3m-sse3 make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 4%] Linking C static library libffindex.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 6%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h [ 8%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 9%] Built target hhviterbialgorithm_with_celloff_and_ss [ 10%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/aa.cc [ 13%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 13%] Built target hhviterbialgorithm_and_ss [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/as.cc make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’: /build/hhsuite-RuXJna/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8: /usr/include/c++/15/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-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-RuXJna/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-RuXJna/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 -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/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-RuXJna/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking C executable ffindex_build cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 26%] Linking C executable ffindex_from_fasta cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 28%] Linking C executable ffindex_get cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 30%] Linking C executable ffindex_modify cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/log.cc [ 33%] Linking C executable ffindex_unpack cd /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 33%] Built target ffindex_unpack [ 34%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/application.cc 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' 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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 36%] Linking C executable ffindex_order cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 38%] Linking CXX static library libCS_OBJECTS.a [ 39%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' /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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 39%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_extract-plain.dir/DependInfo.cmake "--color=" [ 39%] Built target CS_OBJECTS make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_reduce-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/build make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 40%] Building CXX object src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 41%] Building CXX object src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_reduce.cpp [ 42%] Linking CXX executable a3m_reduce-plain cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-plain.dir/link.txt --verbose=1 [ 43%] Linking CXX executable a3m_extract-plain cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 43%] Built target a3m_reduce-plain make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/depend make[4]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_reduce-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 44%] Building CXX object src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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_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[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 44%] Built target a3m_extract-plain make -f 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executable a3m_database_filter-plain cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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_filter-plain.dir/link.d "CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 50%] Built target a3m_database_filter-plain [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd 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/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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 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-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-RuXJna/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhutil.cpp [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/util.cpp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhmm.cpp /build/hhsuite-RuXJna/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-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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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-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-RuXJna/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+ds=. -fstack-protector-strong 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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 -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-plain.dir/link.d "CMakeFiles/hhalign-plain.dir/hhblits_app.cpp.o" -o hhalign-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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 92%] Linking CXX executable hhconsensus-plain cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 93%] Building CXX object src/CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhsearch_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 95%] Building CXX object src/CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhalign_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 97%] Building CXX object src/CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_ca3m-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' [ 99%] Building CXX object src/CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-RuXJna/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, inlined from ‘int main(int, const char**)’ at /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_plain' [100%] Built target hhblits_ca3m-plain [100%] Linking CXX executable cstranslate-plain cd /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+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-RuXJna/hhsuite-3.3.0+ds/build_plain' [100%] Built target cstranslate-plain make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' make[1]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/all make[3]: Entering directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-RuXJna/hhsuite-3.3.0+ds /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/mybuild' [ 33%] Generating ../generated/context_data.crf.h [ 66%] Generating ../generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [100%] Generating ../generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild' [100%] Built target generated make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' rm -Rf /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/testdir mkdir -p /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/testdir cd build_plain/src && \ for file in *-plain ; \ do ln -s /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/src/${file} /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/testdir/${file%%-plain} ; done cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/:/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/testdir ./test.sh - 00:11:40.226 INFO: query.a3m is in A2M, A3M or FASTA format - 00:11:40.933 INFO: Alternative alignment: 0 - 00:11:40.942 INFO: 1 alignments done - 00:11:40.961 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 Sat Oct 18 00:11:41 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 660 0 query.a3m 0 32666 2 0 query.a3m 0 32666 65 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... - 00:11:42.336 INFO: Searching 1 column state sequences. - 00:11:42.382 INFO: query.a3m is in A2M, A3M or FASTA format - 00:11:42.397 INFO: Iteration 1 - 00:11:42.002 INFO: Prefiltering database - 00:11:43.610 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 00:11:43.613 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 00:11:43.613 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 00:11:43.613 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 00:11:43.656 INFO: Alternative alignment: 0 - 00:11:43.664 INFO: 1 alignments done - 00:11:43.664 INFO: Alternative alignment: 1 - 00:11:43.671 INFO: 1 alignments done - 00:11:43.672 INFO: Alternative alignment: 2 - 00:11:43.672 INFO: Alternative alignment: 3 - 00:11:44.321 INFO: Premerge done - 00:11:44.321 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 00:11:44.346 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 Sat Oct 18 00:11:44 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) - 00:11:44.365 INFO: Searching 1 column state sequences. - 00:11:44.439 INFO: Thread 0 query.a3m - 00:11:44.457 INFO: query.a3m is in A2M, A3M or FASTA format - 00:11:44.472 INFO: Iteration 1 - 00:11:45.073 INFO: Prefiltering database - 00:11:45.677 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 - 00:11:45.677 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 - 00:11:45.677 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 - 00:11:45.677 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 00:11:45.696 INFO: Alternative alignment: 0 - 00:11:45.702 INFO: 1 alignments done - 00:11:45.702 INFO: Alternative alignment: 1 - 00:11:45.707 INFO: 1 alignments done - 00:11:45.707 INFO: Alternative alignment: 2 - 00:11:45.707 INFO: Alternative alignment: 3 - 00:11:46.319 INFO: Premerge done - 00:11:46.319 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 00:11:46.337 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 - 00:11:46.406 INFO: query.a3m is in A2M, A3M or FASTA format - 00:11:46.421 INFO: Searching 1 database HHMs without prefiltering - 00:11:46.421 INFO: Iteration 1 - 00:11:47.031 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 00:11:47.081 INFO: Alternative alignment: 0 - 00:11:47.090 INFO: 1 alignments done - 00:11:47.090 INFO: Alternative alignment: 1 - 00:11:47.098 INFO: 1 alignments done - 00:11:47.098 INFO: Alternative alignment: 2 - 00:11:47.098 INFO: Alternative alignment: 3 - 00:11:47.762 INFO: Premerge done - 00:11:47.763 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 00:11:47.788 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 Sat Oct 18 00:11:47 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) - 00:11:47.880 INFO: Thread 0 query.a3m - 00:11:47.896 INFO: query.a3m is in A2M, A3M or FASTA format - 00:11:47.911 INFO: Searching 1 database HHMs without prefiltering - 00:11:47.911 INFO: Iteration 1 - 00:11:48.535 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment - 00:11:48.561 INFO: Alternative alignment: 0 - 00:11:48.566 INFO: 1 alignments done - 00:11:48.566 INFO: Alternative alignment: 1 - 00:11:48.572 INFO: 1 alignments done - 00:11:48.572 INFO: Alternative alignment: 2 - 00:11:48.572 INFO: Alternative alignment: 3 - 00:11:49.192 INFO: Premerge done - 00:11:49.193 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm - 00:11:49.210 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds' mkdir -p /build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx2' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx2 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx2' cd build_avx && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_avx' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_avx' cd build_sse4.1 && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse4.1 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse4.1 -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse4.1' cd build_ssse3 && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_ssse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-ssse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-ssse3 -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_ssse3' cd build_sse3 && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_sse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse3 -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse3 -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_sse3' cd build_plain && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds/build_plain' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-plain -- Installing: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-plain -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/build_plain' mkdir -p /build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data cd mybuild/data && make -j2 install DESTDIR=/build/hhsuite-RuXJna/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-RuXJna/hhsuite-3.3.0+ds -B/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall make[3]: Entering directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild' make[3]: Nothing to be done for 'data/preinstall'. make[3]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq make[2]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds/mybuild/data' make[1]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/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-RuXJna/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-RuXJna/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/hhsuite-RuXJna/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-RuXJna/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/hhsuite-RuXJna/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-9_all.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-9_amd64.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-9_amd64.deb'. dpkg-genbuildinfo -O../hhsuite_3.3.0+ds-9_amd64.buildinfo dpkg-genchanges -O../hhsuite_3.3.0+ds-9_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 2025-10-18T00:20:30Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 18 Oct 2025 00:20:31 +0000 | +------------------------------------------------------------------------------+ hhsuite_3.3.0+ds-9_amd64.changes: --------------------------------- Format: 1.8 Date: Fri, 17 Oct 2025 17:36:29 +0200 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: source all amd64 Version: 3.3.0+ds-9 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hhsuite - sensitive protein sequence searching based on HMM-HMM alignment hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment ( Closes: 1112991 Changes: hhsuite (3.3.0+ds-9) unstable; urgency=medium . * Fix build with CMake 4 Closes: #1112991 * d/watch: version=5 * Standards-Version: 4.7.2 (routine-update) * debputy lint --auto-fix (routine-update) Checksums-Sha1: 3ecf60d9190147ae697e8cd553368e0dffda7381 1245 hhsuite_3.3.0+ds-9.dsc 128e4d8b43032a85c68321b4a4661e17c1f23044 16904 hhsuite_3.3.0+ds-9.debian.tar.xz d44daca7409b25e92eea6ff8f2dfbd70a745bf7b 4401984 hhsuite-data_3.3.0+ds-9_all.deb 22e79f760a8f8e33b8f035ee65a9c6535ac5e21a 126864676 hhsuite-dbgsym_3.3.0+ds-9_amd64.deb c9dd6b0c6b622996ba6a8d2721e43a6886f4f96b 7868 hhsuite_3.3.0+ds-9_amd64.buildinfo 4475c1bfe5e180cd7daf378ce485d9400a0ac82d 57486736 hhsuite_3.3.0+ds-9_amd64.deb Checksums-Sha256: d856b3a6da42612debfe2387f3d07cc542518ec1c5252d2b4c4c940fff4cf740 1245 hhsuite_3.3.0+ds-9.dsc 930c7195042d4c83975b99039a4df4904041a557a8d142f38dcc94f4ecc3f900 16904 hhsuite_3.3.0+ds-9.debian.tar.xz 14e5361537874eb5582dcbc919ad35ea3467257d8fb2302f1849512e4fbe2fae 4401984 hhsuite-data_3.3.0+ds-9_all.deb ef421d93362119e149e51b32b4abd91b0e583b34b9b321ddf24e8c3cf61419fc 126864676 hhsuite-dbgsym_3.3.0+ds-9_amd64.deb a3fad366294cc81a8705a11bb65c2739b3b658b9dc57bba4b843a9d2a3c60e0a 7868 hhsuite_3.3.0+ds-9_amd64.buildinfo 1263659401fe87b8d2b59c3ffb80578faf3fa7f5cad3a2fa80ff6bc4fb351d17 57486736 hhsuite_3.3.0+ds-9_amd64.deb Files: d5a531b20414ed759891b548a3866788 1245 science optional hhsuite_3.3.0+ds-9.dsc 4bb89a0a1a1f74616d3a20353441f119 16904 science optional hhsuite_3.3.0+ds-9.debian.tar.xz 60efb3bba649f78b1163675976702217 4401984 science optional hhsuite-data_3.3.0+ds-9_all.deb fb0572975bcbe37da4370087eb57137a 126864676 debug optional hhsuite-dbgsym_3.3.0+ds-9_amd64.deb 8808475a2d2c53939be87249d225590a 7868 science optional hhsuite_3.3.0+ds-9_amd64.buildinfo d2d0848106dc1307ea9a97d1e457342f 57486736 science optional hhsuite_3.3.0+ds-9_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 18 Oct 2025 00:20:31 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: hhsuite Binary: hhsuite hhsuite-data hhsuite-dbgsym Architecture: all amd64 source Version: 3.3.0+ds-9 Checksums-Md5: d5a531b20414ed759891b548a3866788 1245 hhsuite_3.3.0+ds-9.dsc 60efb3bba649f78b1163675976702217 4401984 hhsuite-data_3.3.0+ds-9_all.deb fb0572975bcbe37da4370087eb57137a 126864676 hhsuite-dbgsym_3.3.0+ds-9_amd64.deb d2d0848106dc1307ea9a97d1e457342f 57486736 hhsuite_3.3.0+ds-9_amd64.deb Checksums-Sha1: 3ecf60d9190147ae697e8cd553368e0dffda7381 1245 hhsuite_3.3.0+ds-9.dsc d44daca7409b25e92eea6ff8f2dfbd70a745bf7b 4401984 hhsuite-data_3.3.0+ds-9_all.deb 22e79f760a8f8e33b8f035ee65a9c6535ac5e21a 126864676 hhsuite-dbgsym_3.3.0+ds-9_amd64.deb 4475c1bfe5e180cd7daf378ce485d9400a0ac82d 57486736 hhsuite_3.3.0+ds-9_amd64.deb Checksums-Sha256: d856b3a6da42612debfe2387f3d07cc542518ec1c5252d2b4c4c940fff4cf740 1245 hhsuite_3.3.0+ds-9.dsc 14e5361537874eb5582dcbc919ad35ea3467257d8fb2302f1849512e4fbe2fae 4401984 hhsuite-data_3.3.0+ds-9_all.deb ef421d93362119e149e51b32b4abd91b0e583b34b9b321ddf24e8c3cf61419fc 126864676 hhsuite-dbgsym_3.3.0+ds-9_amd64.deb 1263659401fe87b8d2b59c3ffb80578faf3fa7f5cad3a2fa80ff6bc4fb351d17 57486736 hhsuite_3.3.0+ds-9_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 18 Oct 2025 00:20:29 +0000 Build-Path: /build/hhsuite-RuXJna/hhsuite-3.3.0+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-2), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.3-1), binutils (= 2.45-7), binutils-common (= 2.45-7), binutils-x86-64-linux-gnu (= 2.45-7), bsdextrautils (= 2.41.2-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), cmake (= 4.1.1+really3.31.6-2), cmake-data (= 4.1.1+really3.31.6-2), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-14 (= 14.3.0-8), cpp-14-x86-64-linux-gnu (= 14.3.0-8), cpp-15 (= 15.2.0-4), cpp-15-x86-64-linux-gnu (= 15.2.0-4), cpp-x86-64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), fontconfig-config (= 2.15.0-2.4), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-4), g++-15-x86-64-linux-gnu (= 15.2.0-4), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-14 (= 14.3.0-8), gcc-14-base (= 14.3.0-8), gcc-14-x86-64-linux-gnu (= 14.3.0-8), gcc-15 (= 15.2.0-4), gcc-15-base (= 15.2.0-4), gcc-15-x86-64-linux-gnu (= 15.2.0-4), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.12-1), groff-base (= 1.23.0-9), gzip (= 1.13-1), help2man (= 1.49.3), hicolor-icon-theme (= 0.18-2), hostname (= 3.25), imagemagick (= 8:7.1.2.3+dfsg1-1+b1), imagemagick-7-common (= 8:7.1.2.3+dfsg1-1), imagemagick-7.q16 (= 8:7.1.2.3+dfsg1-1+b1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-4+b1), libasan8 (= 15.2.0-4), libatomic1 (= 15.2.0-4), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1), libbinutils (= 2.45-7), libblkid1 (= 2.41.2-4), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-4), libcom-err2 (= 1.47.2-3+b3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-7), libctf0 (= 2.45-7), libcurl4t64 (= 8.16.0-4), libdav1d7 (= 1.5.1-1), libdb5.3t64 (= 5.3.28+dfsg2-10), libde265-0 (= 1.0.16-1), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.28), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.193-3), libexpat1 (= 2.7.3-1), libffi8 (= 3.5.2-2), libfftw3-double3 (= 3.3.10-2+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libfontconfig1 (= 2.15.0-2.4), libfreetype6 (= 2.13.3+dfsg-1), libgcc-14-dev (= 14.3.0-8), libgcc-15-dev (= 15.2.0-4), libgcc-s1 (= 15.2.0-4), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libglib2.0-0t64 (= 2.86.0-5), libgmp10 (= 2:6.3.0+dfsg-5), libgnutls30t64 (= 3.8.10-2), libgomp1 (= 15.2.0-4), libgprofng0 (= 2.45-7), libgssapi-krb5-2 (= 1.21.3-5), libheif-plugin-dav1d (= 1.20.2-2+b1), libheif-plugin-libde265 (= 1.20.2-2+b1), libheif1 (= 1.20.2-2+b1), libhogweed6t64 (= 3.10.2-1), libhwasan0 (= 15.2.0-4), libidn2-0 (= 2.3.8-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-4), libjansson4 (= 2.14-2+b3), libjbig0 (= 2.1-6.1+b2), libjpeg62-turbo (= 1:2.1.5-4), libjsoncpp26 (= 1.9.6-4), libk5crypto3 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblcms2-2 (= 2.16-2), libldap2 (= 2.6.10+dfsg-1+b1), liblerc4 (= 4.0.0+ds-5), liblocale-gettext-perl (= 1.07-7+b2), liblqr-1-0 (= 0.4.2-2.1+b2), liblsan0 (= 15.2.0-4), libltdl7 (= 2.5.4-5), liblz4-1 (= 1.10.0-4), liblzma5 (= 5.8.1-2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmagickcore-7.q16-10 (= 8:7.1.2.3+dfsg1-1+b1), libmagickwand-7.q16-10 (= 8:7.1.2.3+dfsg1-1+b1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-4), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.12.0-1), libngtcp2-16 (= 1.16.0-1), libngtcp2-crypto-ossl0 (= 1.16.0-1), libopenjp2-7 (= 2.5.3-2.1), libp11-kit0 (= 0.25.9-2), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.46-1), libperl5.42 (= 5.42.0-2), libpipeline1 (= 1.5.8-1), libpng16-16t64 (= 1.6.50-1), libproc2-0 (= 2:4.0.4-9), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 15.2.0-4), libraw23t64 (= 0.21.4-2), librhash1 (= 1.4.6-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-7), libsharpyuv0 (= 1.5.0-0.1), libsimde-dev (= 0.8.2-3), libsmartcols1 (= 2.41.2-4), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-4), libstdc++6 (= 15.2.0-4), libsystemd0 (= 258.1-1), libtasn1-6 (= 4.20.0-2), libtiff6 (= 4.7.1-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-5), libtsan2 (= 15.2.0-4), libubsan1 (= 15.2.0-4), libuchardet0 (= 0.0.8-2), libudev1 (= 258.1-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-4), libuv1t64 (= 1.51.0-2), libwebp7 (= 1.5.0-0.1), libwebpdemux2 (= 1.5.0-0.1), libwebpmux3 (= 1.5.0-0.1), libx11-6 (= 2:1.8.12-1), libx11-data (= 2:1.8.12-1), 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), libxml2-16 (= 2.14.6+dfsg-0.1), libxxhash0 (= 0.8.3-2), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.16.12-2), m4 (= 1.4.20-2), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.42.0-2), perl-base (= 5.42.0-2), perl-modules-5.42 (= 5.42.0-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-9), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.2-4), xz-utils (= 5.8.1-2), 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="1760715389" +------------------------------------------------------------------------------+ | Package contents Sat, 18 Oct 2025 00:20:31 +0000 | +------------------------------------------------------------------------------+ hhsuite-data_3.3.0+ds-9_all.deb ------------------------------- new Debian package, version 2.0. size 4401984 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-9 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). . 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Installed-Size: 468095 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 14), perl:any, hhsuite-data (= 3.3.0+ds-9), python3 Conflicts: ffindex Built-Using: simde (= 0.8.2-3) 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 2025-10-17 15:36 ./ drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/bin/ lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/a3m_database_extract -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/a3m_database_filter -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/a3m_database_reduce -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/a3m_extract -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/a3m_reduce -> ../libexec/hhsuite/simd-dispatch -rwxr-xr-x root/root 31136 2025-10-17 15:36 ./usr/bin/ffindex_apply -rwxr-xr-x root/root 31200 2025-10-17 15:36 ./usr/bin/ffindex_build -rwxr-xr-x root/root 26976 2025-10-17 15:36 ./usr/bin/ffindex_from_fasta -rwxr-xr-x root/root 30960 2025-10-17 15:36 ./usr/bin/ffindex_from_fasta_with_split -rwxr-xr-x root/root 26944 2025-10-17 15:36 ./usr/bin/ffindex_get -rwxr-xr-x root/root 27040 2025-10-17 15:36 ./usr/bin/ffindex_modify -rwxr-xr-x root/root 22768 2025-10-17 15:36 ./usr/bin/ffindex_order -rwxr-xr-x root/root 22768 2025-10-17 15:36 ./usr/bin/ffindex_reduce -rwxr-xr-x root/root 22768 2025-10-17 15:36 ./usr/bin/ffindex_unpack lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhalign -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhalign_omp -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhblits -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhblits_ca3m -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhblits_omp -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhconsensus -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhfilter -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhmake -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhsearch -> ../libexec/hhsuite/simd-dispatch lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/bin/hhsearch_omp -> ../libexec/hhsuite/simd-dispatch drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/lib/ lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/lib/hh -> hhsuite drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/lib/hhsuite/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./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 2025-10-17 15:36 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/libexec/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/libexec/hhsuite/ -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-avx -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-avx2 -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-plain -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-sse3 -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-sse4.1 -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_extract-ssse3 -rwxr-xr-x root/root 63896 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-avx -rwxr-xr-x root/root 63896 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-avx2 -rwxr-xr-x root/root 59800 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-plain -rwxr-xr-x root/root 59800 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-sse3 -rwxr-xr-x root/root 63896 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-sse4.1 -rwxr-xr-x root/root 59800 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_filter-ssse3 -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-avx -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-avx2 -rwxr-xr-x root/root 51608 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-plain -rwxr-xr-x root/root 51608 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-sse3 -rwxr-xr-x root/root 55704 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-sse4.1 -rwxr-xr-x root/root 51608 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_database_reduce-ssse3 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-avx -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-avx2 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-plain -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-sse3 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-sse4.1 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_extract-ssse3 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-avx -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-avx2 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-plain -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-sse3 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-sse4.1 -rwxr-xr-x root/root 51528 2025-10-17 15:36 ./usr/libexec/hhsuite/a3m_reduce-ssse3 drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/libexec/hhsuite/bin/ lrwxrwxrwx root/root 0 2025-10-17 15:36 ./usr/libexec/hhsuite/bin/cstranslate -> ../simd-dispatch -rwxr-xr-x root/root 6281704 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-avx -rwxr-xr-x root/root 6277608 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-avx2 -rwxr-xr-x root/root 6265320 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-plain -rwxr-xr-x root/root 6265320 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-sse3 -rwxr-xr-x root/root 6277608 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-sse4.1 -rwxr-xr-x root/root 6265320 2025-10-17 15:36 ./usr/libexec/hhsuite/cstranslate-ssse3 -rwxr-xr-x root/root 8255912 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-avx -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-avx2 -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-plain -rwxr-xr-x root/root 8223144 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-sse3 -rwxr-xr-x root/root 8255912 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-sse4.1 -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign-ssse3 -rwxr-xr-x root/root 8264104 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-avx -rwxr-xr-x root/root 8235432 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-avx2 -rwxr-xr-x root/root 8231336 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-plain -rwxr-xr-x root/root 8231336 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-sse3 -rwxr-xr-x root/root 8264104 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-sse4.1 -rwxr-xr-x root/root 8231336 2025-10-17 15:36 ./usr/libexec/hhsuite/hhalign_omp-ssse3 -rwxr-xr-x root/root 8206760 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-avx -rwxr-xr-x root/root 8178088 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-avx2 -rwxr-xr-x root/root 8178088 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-plain -rwxr-xr-x root/root 8178088 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-sse3 -rwxr-xr-x root/root 8206760 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-sse4.1 -rwxr-xr-x root/root 8178088 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits-ssse3 -rwxr-xr-x root/root 8210856 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-avx -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-avx2 -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-plain -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-sse3 -rwxr-xr-x root/root 8210856 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-sse4.1 -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_ca3m-ssse3 -rwxr-xr-x root/root 8214952 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-avx -rwxr-xr-x root/root 8186280 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-avx2 -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-plain -rwxr-xr-x root/root 8182184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-sse3 -rwxr-xr-x root/root 8214952 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-sse4.1 -rwxr-xr-x root/root 8186280 2025-10-17 15:36 ./usr/libexec/hhsuite/hhblits_omp-ssse3 -rwxr-xr-x root/root 7670184 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-avx -rwxr-xr-x root/root 7657896 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-avx2 -rwxr-xr-x root/root 7641512 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-plain -rwxr-xr-x root/root 7641512 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-sse3 -rwxr-xr-x root/root 7666088 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-sse4.1 -rwxr-xr-x root/root 7641512 2025-10-17 15:36 ./usr/libexec/hhsuite/hhconsensus-ssse3 -rwxr-xr-x root/root 371104 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-avx -rwxr-xr-x root/root 367008 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-avx2 -rwxr-xr-x root/root 358816 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-plain -rwxr-xr-x root/root 358816 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-sse3 -rwxr-xr-x root/root 367008 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-sse4.1 -rwxr-xr-x root/root 358816 2025-10-17 15:36 ./usr/libexec/hhsuite/hhfilter-ssse3 -rwxr-xr-x root/root 7645608 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-avx -rwxr-xr-x root/root 7633320 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-avx2 -rwxr-xr-x root/root 7616936 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-plain -rwxr-xr-x root/root 7616936 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-sse3 -rwxr-xr-x root/root 7641512 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-sse4.1 -rwxr-xr-x root/root 7616936 2025-10-17 15:36 ./usr/libexec/hhsuite/hhmake-ssse3 -rwxr-xr-x root/root 8247720 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-avx -rwxr-xr-x root/root 8219048 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-avx2 -rwxr-xr-x root/root 8214952 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-plain -rwxr-xr-x root/root 8214952 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-sse3 -rwxr-xr-x root/root 8247720 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-sse4.1 -rwxr-xr-x root/root 8214952 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch-ssse3 -rwxr-xr-x root/root 8251816 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-avx -rwxr-xr-x root/root 8223144 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-avx2 -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-plain -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-sse3 -rwxr-xr-x root/root 8255912 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-sse4.1 -rwxr-xr-x root/root 8227240 2025-10-17 15:36 ./usr/libexec/hhsuite/hhsearch_omp-ssse3 -rwxr-xr-x root/root 453 2025-10-17 15:36 ./usr/libexec/hhsuite/simd-dispatch drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/share/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./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 1909 2025-10-17 15:36 ./usr/share/doc/hhsuite/changelog.Debian.gz -rw-r--r-- root/root 20399 2025-10-17 15:36 ./usr/share/doc/hhsuite/copyright drwxr-xr-x root/root 0 2025-10-17 15:36 ./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 2025-10-17 15:36 ./usr/share/hhsuite/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./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 2025-10-17 15:36 ./usr/share/hhsuite/scripts/a3m.py -rwxr-xr-x root/root 31681 2025-10-17 15:36 ./usr/share/hhsuite/scripts/addss.pl -rwxr-xr-x root/root 438 2025-10-17 15:36 ./usr/share/hhsuite/scripts/check_a3m.py -rwxr-xr-x root/root 28735 2025-10-17 15:36 ./usr/share/hhsuite/scripts/cif2fasta.py -rwxr-xr-x root/root 4654 2025-10-17 15:36 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl -rwxr-xr-x root/root 6815 2025-10-17 15:36 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl -rwxr-xr-x root/root 2081 2025-10-17 15:36 ./usr/share/hhsuite/scripts/ffindex.py -rwxr-xr-x root/root 446 2025-10-17 15:36 ./usr/share/hhsuite/scripts/get_a3m_size.py -rwxr-xr-x root/root 7179 2025-10-17 15:36 ./usr/share/hhsuite/scripts/hh_reader.py -rwxr-xr-x root/root 48079 2025-10-17 15:36 ./usr/share/hhsuite/scripts/hhmakemodel.pl -rwxr-xr-x root/root 87343 2025-10-17 15:36 ./usr/share/hhsuite/scripts/hhmakemodel.py -rwxr-xr-x root/root 16961 2025-10-17 15:36 ./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 2025-10-17 15:36 ./usr/share/hhsuite/scripts/multithread.pl -rwxr-xr-x root/root 40490 2025-10-17 15:36 ./usr/share/hhsuite/scripts/pdb2fasta.pl -rwxr-xr-x root/root 13183 2025-10-17 15:36 ./usr/share/hhsuite/scripts/pdbfilter.pl -rwxr-xr-x root/root 8648 2025-10-17 15:36 ./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 2025-10-17 15:36 ./usr/share/hhsuite/scripts/renumberpdb.pl -rwxr-xr-x root/root 3651 2025-10-17 15:36 ./usr/share/hhsuite/scripts/splitfasta.pl drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/share/man/ drwxr-xr-x root/root 0 2025-10-17 15:36 ./usr/share/man/man1/ -rw-r--r-- root/root 3089 2025-10-17 15:36 ./usr/share/man/man1/hhalign.1.gz -rw-r--r-- root/root 4141 2025-10-17 15:36 ./usr/share/man/man1/hhblits.1.gz -rw-r--r-- root/root 4152 2025-10-17 15:36 ./usr/share/man/man1/hhblits_omp.1.gz -rw-r--r-- root/root 1029 2025-10-17 15:36 ./usr/share/man/man1/hhconsensus.1.gz -rw-r--r-- root/root 1022 2025-10-17 15:36 ./usr/share/man/man1/hhfilter.1.gz -rw-r--r-- root/root 1655 2025-10-17 15:36 ./usr/share/man/man1/hhmake.1.gz -rw-r--r-- root/root 3358 2025-10-17 15:36 ./usr/share/man/man1/hhsearch.1.gz +------------------------------------------------------------------------------+ | Post Build Sat, 18 Oct 2025 00:20:37 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sat, 18 Oct 2025 00:20:37 +0000 | +------------------------------------------------------------------------------+ Purging /build/hhsuite-RuXJna Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 18 Oct 2025 00:20:39 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 3785968 Build-Time: 1117 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/hhsuite_3.3.0+ds-9.dsc Machine Architecture: amd64 Package: hhsuite Package-Time: 1129 Source-Version: 3.3.0+ds-9 Space: 3785968 Status: successful Version: 3.3.0+ds-9 -------------------------------------------------------------------------------- Finished at 2025-10-18T00:20:30Z Build needed 00:18:49, 3785968k disk space