sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | sga 0.10.15-7 (amd64) Sun, 12 Jul 2026 01:47:04 +0000 | +==============================================================================+ Package: sga Version: 0.10.15-7 Source Version: 0.10.15-7 Distribution: perl-5.44-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 Sun, 12 Jul 2026 01:47:05 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup sga_0.10.15-7 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup sga_0.10.15-7 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 12 Jul 2026 01:47:05 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 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 Sun, 12 Jul 2026 01:47:12 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/sga_0.10.15-7.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 12 Jul 2026 01:47:13 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/sga-lJTTar/resolver-GCtNxD/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ InRelease Get:2 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ Release [609 B] Ign:3 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ Release.gpg Get:4 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ Sources [774 B] Get:5 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ Packages [758 B] Fetched 2141 B in 0s (147 kB/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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base graphviz groff-base help2man intltool-debian libabsl20260107 libaom3 libarchive-zip-perl libavif16 libbamtools-dev libbamtools2.5.3 libbrotli1 libcairo2 libcdt6 libcgraph8 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libdatrie1 libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-2 libgd3 libglib2.0-0t64 libgraphite2-3 libgssapi-krb5-2 libgvc7 libgvplugin-gd8 libgvplugin-pango8 libgvpr2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librav1e0.8 libsharpyuv0 libsparsehash-dev libssh2-1t64 libsvtav1enc4 libthai-data libthai0 libtiff6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2-16 libxpm4 libxrender1 libyuv0 m4 man-db media-types netbase po-debconf python3 python3-minimal python3-pysam python3-ruffus python3.14 python3.14-minimal samtools sensible-utils tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n gsfonts graphviz-doc groff libbamtools-doc libgd-tools 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 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binfmt-support cwltool Recommended packages: curl | wget | lynx fonts-liberation ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libheif-plugin-x265 libheif-plugin-aomenc krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base graphviz groff-base help2man intltool-debian libabsl20260107 libaom3 libarchive-zip-perl libavif16 libbamtools-dev libbamtools2.5.3 libbrotli1 libcairo2 libcdt6 libcgraph8 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libdatrie1 libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-2 libgd3 libglib2.0-0t64 libgraphite2-3 libgssapi-krb5-2 libgvc7 libgvplugin-gd8 libgvplugin-pango8 libgvpr2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librav1e0.8 libsharpyuv0 libsparsehash-dev libssh2-1t64 libsvtav1enc4 libthai-data libthai0 libtiff6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2-16 libxpm4 libxrender1 libyuv0 m4 man-db media-types netbase po-debconf python3 python3-minimal python3-pysam python3-ruffus python3.14 python3.14-minimal samtools sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 46.4 MB/47.2 MB of archives. After this operation, 194 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 liblocale-gettext-perl amd64 1.07-10+b1 [15.1 kB] Get:2 copy:/build/sga-lJTTar/resolver-GCtNxD/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Get:4 file:/srv/reprepro perl-5.44/main amd64 libcdt6 amd64 14.1.2-1+b3 [18.3 kB] Get:5 file:/srv/reprepro perl-5.44/main amd64 libcgraph8 amd64 14.1.2-1+b3 [58.5 kB] Get:6 file:/srv/reprepro perl-5.44/main amd64 libpathplan4 amd64 14.1.2-1+b3 [29.6 kB] Get:7 file:/srv/reprepro perl-5.44/main amd64 libxdot4 amd64 14.1.2-1+b3 [21.5 kB] Get:8 file:/srv/reprepro perl-5.44/main amd64 libgvc7 amd64 14.1.2-1+b3 [375 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.6-1 [896 kB] Get:10 file:/srv/reprepro perl-5.44/main amd64 libgvpr2 amd64 14.1.2-1+b3 [125 kB] Get:11 file:/srv/reprepro perl-5.44/main amd64 libgvplugin-gd8 amd64 14.1.2-1+b3 [26.9 kB] Get:12 file:/srv/reprepro perl-5.44/main amd64 libgvplugin-pango8 amd64 14.1.2-1+b3 [31.2 kB] Get:13 file:/srv/reprepro perl-5.44/main amd64 graphviz amd64 14.1.2-1+b3 [60.2 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.6-1 [2416 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.6-1 [25.1 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.6-1 [2278 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.6-1 [846 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.6-1 [8108 B] Get:22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.6-1 [25.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260623 [114 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.58-1 [289 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.14.3+dfsg-1 [493 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-9 [488 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-9 [840 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.17.1-5 [191 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.46.4-1+b2 [259 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1+b2 [27.7 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-3+b1 [543 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.13.1-2+b1 [1904 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.3-1+b2 [563 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libabsl20260107 amd64 20260107.0-5 [549 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libgav1-2 amd64 0.20.0-2+b1 [372 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librav1e0.8 amd64 0.8.1-10 [973 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc4 amd64 4.1.0+dfsg-1 [2414 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1949.20260706-1 [177 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.4.2-1 [147 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b2 [115 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.1.1-1 [201 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.23.1-1 [17.3 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.23.1-1 [19.8 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.23.1-1 [761 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.1-1+b2 [255 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.1.1+ds-1 [199 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1+b2 [335 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.2-1 [383 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.19-1 [58.9 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-13+b2 [126 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.88.2-1 [1536 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-5+b1 [26.2 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.15-2 [75.8 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 12.3.2-2+b2 [513 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.30-2 [172 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.14-2 [39.1 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.30-2 [51.8 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.58.0-1 [225 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.58.0-1 [53.1 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.58.0-1 [34.2 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.3 amd64 2.5.3+dfsg-2 [161 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.3+dfsg-2 [223 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:114 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20260608-2 [107 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.4-1 [76.9 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.3+ds-2+b1 [4456 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 python3-ruffus all 2.8.4-8 [151 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Preconfiguring packages ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../116-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up libxdot4:amd64 (14.1.2-1+b3) ... Setting up libgraphite2-3:amd64 (1.3.15-2) ... Setting up libcdt6:amd64 (14.1.2-1+b3) ... Setting up libpixman-1-0:amd64 (0.46.4-1+b2) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1+b2) ... Setting up libaom3:amd64 (3.13.1-2+b1) ... Setting up libxau6:amd64 (1:1.0.11-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.5-2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libxcb1:amd64 (1.17.0-2+b2) ... Setting up liblerc4:amd64 (4.1.1+ds-1) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libdatrie1:amd64 (0.2.14-2) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libxcb-render0:amd64 (1.17.0-2+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.3) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libpsl5t64:amd64 (0.22.0-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up gettext-base (1.0-3) ... Setting up m4 (1.4.21-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b2) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.47-4) ... Setting up libsparsehash-dev (2.0.4-1) ... Setting up libjbig0:amd64 (2.1-6.1+b3) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up librav1e0.8:amd64 (0.8.1-10) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jul 12 01:47:29 UTC 2026. Universal Time is now: Sun Jul 12 01:47:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up libglib2.0-0t64:amd64 (2.88.2-1) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:amd64 (1:3.1.3-4) ... Setting up libx11-data (2:1.8.13-1) ... Setting up libpathplan4:amd64 (14.1.2-1+b3) ... Setting up libncurses6:amd64 (6.6+20260608-2) ... Setting up libfribidi0:amd64 (1.0.16-5+b1) ... Setting up libimagequant0:amd64 (4.4.1-1+b2) ... Setting up fonts-dejavu-mono (2.37-9) ... Setting up libpng16-16t64:amd64 (1.6.58-1) ... Setting up autopoint (1.0-3) ... Setting up fonts-dejavu-core (2.37-9) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libltdl7:amd64 (2.5.4-11) ... Setting up libsvtav1enc4:amd64 (4.1.0+dfsg-1) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libcgraph8:amd64 (14.1.2-1+b3) ... Setting up libwebp7:amd64 (1.5.0-0.1+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libgvpr2:amd64 (14.1.2-1+b3) ... Setting up dwz (0.16-4) ... Setting up libbamtools2.5.3:amd64 (2.5.3+dfsg-2) ... Setting up libdav1d7:amd64 (1.5.3-1+b2) ... Setting up sensible-utils (0.0.26) ... Setting up libtiff6:amd64 (4.7.2-1) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libx11-6:amd64 (2:1.8.13-1) ... Setting up libthai-data (0.1.30-2) ... Setting up libabsl20260107:amd64 (20260107.0-5) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libde265-0:amd64 (1.1.1-1) ... Setting up libyuv0:amd64 (0.0.1949.20260706-1) ... Setting up liblocale-gettext-perl (1.07-10+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libxpm4:amd64 (1:3.5.19-1) ... Setting up libxrender1:amd64 (1:0.9.12-1+b2) ... Setting up libtool (2.5.4-11) ... Setting up libpython3.14-stdlib:amd64 (3.14.6-1) ... Setting up fontconfig-config (2.17.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (22) ... Setting up libthai0:amd64 (0.1.30-2) ... Setting up libfreetype6:amd64 (2.14.3+dfsg-1) ... Setting up libbamtools-dev:amd64 (2.5.3+dfsg-2) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libgvc7:amd64 (14.1.2-1+b3) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up libgav1-2:amd64 (0.20.0-2+b1) ... Setting up groff-base (1.24.1-1) ... Setting up libharfbuzz0b:amd64 (12.3.2-2+b2) ... Setting up libfontconfig1:amd64 (2.17.1-5) ... Setting up python3.14 (3.14.6-1) ... Setting up libpython3-stdlib:amd64 (3.14.6-1) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up fontconfig (2.17.1-5) ... Regenerating fonts cache... done. Setting up libavif16:amd64 (1.4.2-1) ... Setting up po-debconf (1.0.22) ... Setting up libpango-1.0-0:amd64 (1.58.0-1) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up python3 (3.14.6-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.4-3+b1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.58.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.58.0-1) ... Setting up dh-python (7.20260623) ... Setting up python3-pysam (0.23.3+ds-2+b1) ... Setting up libgvplugin-pango8:amd64 (14.1.2-1+b3) ... Setting up debhelper (14.3) ... Setting up samtools (1.22.1-1) ... Setting up libheif-plugin-libde265:amd64 (1.23.1-1) ... Setting up libheif-plugin-dav1d:amd64 (1.23.1-1) ... Setting up libheif1:amd64 (1.23.1-1) ... Setting up libgd3:amd64 (2.3.3-13+b2) ... Setting up libgvplugin-gd8:amd64 (14.1.2-1+b3) ... Setting up graphviz (14.1.2-1+b3) ... Setting up python3-ruffus (2.8.4-8) ... /usr/lib/python3/dist-packages/ruffus/test/draw_specified_dependency_tree.py:112: SyntaxWarning: "\[" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\["? A raw string is also an option. attributes = re.compile("\[.+\]") Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... Processing triggers for systemd (261.1-2) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 12 Jul 2026 01:47:35 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 12 Jul 2026 01:47:35 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260623 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 fontconfig_2.17.1-5 fontconfig-config_2.17.1-5 fonts-dejavu-core_2.37-9 fonts-dejavu-mono_2.37-9 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7 gpg-agent_2.4.9-7 gpgconf_2.4.9-7 gpgsm_2.4.9-7 graphviz_14.1.2-1+b3 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libabsl20260107_20260107.0-5 libacl1_2.4.0-1 libaom3_3.13.1-2+b1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libavif16_1.4.2-1 libbamtools-dev_2.5.3+dfsg-2 libbamtools2.5.3_2.5.3+dfsg-2 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcairo2_1.18.4-3+b1 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcdt6_14.1.2-1+b3 libcgraph8_14.1.2-1+b3 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl3t64-gnutls_8.21.0-2 libcurl4-gnutls_8.21.0-2 libdatrie1_0.2.14-2 libdav1d7_1.5.3-1+b2 libdb5.3t64_5.3.28+dfsg2-11+b1 libde265-0_1.1.1-1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libexpat1_2.8.2-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libfontconfig1_2.17.1-5 libfreetype6_2.14.3+dfsg-1 libfribidi0_1.0.16-5+b1 libgav1-2_0.20.0-2+b1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgd3_2.3.3-13+b2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libglib2.0-0t64_2.88.2-1 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgraphite2-3_1.3.15-2 libgssapi-krb5-2_1.22.1-3 libgvc7_14.1.2-1+b3 libgvplugin-gd8_14.1.2-1+b3 libgvplugin-pango8_14.1.2-1+b3 libgvpr2_14.1.2-1+b3 libharfbuzz0b_12.3.2-2+b2 libheif-plugin-dav1d_1.23.1-1 libheif-plugin-libde265_1.23.1-1 libheif1_1.23.1-1 libhogweed6t64_3.10.2-1+b1 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libimagequant0_4.4.1-1+b2 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libjbig0_2.1-6.1+b3 libjpeg62-turbo_1:3.1.3-4 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap2_2.6.13+dfsg-1+b1 liblerc4_4.1.1+ds-1 liblocale-gettext-perl_1.07-10+b1 liblsan0_16.1.0-2 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses6_6.6+20260608-2 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit0_0.26.4-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpango-1.0-0_1.58.0-1 libpangocairo-1.0-0_1.58.0-1 libpangoft2-1.0-0_1.58.0-1 libpathplan4_14.1.2-1+b3 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libpixman-1-0_0.46.4-1+b2 libpng16-16t64_1.6.58-1 libpsl5t64_0.22.0-1 libpython3-stdlib_3.14.6-1 libpython3.14-minimal_3.14.6-1 libpython3.14-stdlib_3.14.6-1 libquadmath0_16.1.0-2 librav1e0.8_0.8.1-10 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsframe3_2.46.50.20260617-1 libsharpyuv0_1.5.0-0.1+b2 libsmartcols1_2.42.2-1 libsparsehash-dev_2.0.4-1 libsqlite3-0_3.53.3-1 libssh2-1t64_1.11.1-4 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsvtav1enc4_4.1.0+dfsg-1 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libthai-data_0.1.30-2 libthai0_0.1.30-2 libtiff6_4.7.2-1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libwebp7_1.5.0-0.1+b2 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb-render0_1.17.0-2+b2 libxcb-shm0_1.17.0-2+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxdot4_14.1.2-1+b3 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.3+dfsg-1 libxpm4_1:3.5.19-1 libxrender1_1:0.9.12-1+b2 libxxhash0_0.8.3-2+b2 libyuv0_0.0.1949.20260706-1 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.42.2-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.5 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.3-2 po-debconf_1.0.22 python3_3.14.6-1 python3-minimal_3.14.6-1 python3-pysam_0.23.3+ds-2+b1 python3-ruffus_2.8.4-8 python3.14_3.14.6-1 python3.14-minimal_3.14.6-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 systemd_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 tzdata_2026b-1 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 12 Jul 2026 01:47:35 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sga Binary: sga Architecture: any Version: 0.10.15-7 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://github.com/jts/sga Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/sga Vcs-Git: https://salsa.debian.org/med-team/sga.git Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools , python3 , python3-ruffus , python3-pysam Package-List: sga deb science optional arch=any Checksums-Sha1: 55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz 4598b0bf58446b932f202a8bfa7e9d9d3bc018de 214356 sga_0.10.15-7.debian.tar.xz Checksums-Sha256: 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 6569986 sga_0.10.15.orig.tar.gz 708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 214356 sga_0.10.15-7.debian.tar.xz Files: 990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz 420c1f46b48f89950ac7e500402215e8 214356 sga_0.10.15-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmFEoJwACgkQPCZ2P2xn 5uIThw/5AcAmhXJYwdZ93J6fhmzcEOSTkqi8GdH/9Nlt3BCVIZlJR3/6vcttoVUo sKob/Rr78LGESV215LOC13J9soUrZa6giB6aM+wU+hVhD81dCt7zz2bsMSvwopC8 DNmWt3cZta4xDM7MxuBL5cztJZThE8ewwbZ3VQmGHix/aAMOlcK2EsP9iQCpRepF Ovmc4kDe1USc6erpE3cohGVlHfoJy4JXggHjvKqHz4u4YGFLQNpHpT70LH9HSrgh thqrPnnI9I2CjNxF2WSYIFMCD5f1Iq9TWihNi4H6m0keRgZcFE1lKjKuP8WYT9rK GLvaAGaLC1sB0BZ0lLpf18pySxNUzA/EtX6RzBes0UMRG9SkWG2lOFTyZRJjhC/3 Mz3FGKLROVKjTOerTgdhDKCoAPa/VLwXIYZLX/xxHxVelJibqPHRlWuS6xaJkunW OzPueUfUSynrS9kQZ5bM0CIfmhl+9zqWKNIfvwRDqmTh5meaH/oYneMgUIKSJgLa PBU8/Qc+FzpObFe71EIRa/5vs+kUQcvLIoeFqYMoDLd5WFwyFlTTe035u4SKpA7q EOADJZbbLzqBP89tgkWjglsUCVClDBUeyuocQXREI85kW9GkoWnwvKqkZaRNncxO UdqDEwW4NwADMhzii6hdLiJxBiYBhcLkP+ciz4TxX2wUKU6qO1U= =KU9x -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./sga_0.10.15-7.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./sga_0.10.15-7.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting sga in /build/sga-lJTTar/sga-0.10.15 dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz dpkg-source: info: unpacking sga_0.10.15-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002-no-rpath.patch dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch dpkg-source: info: applying 0006-remove-google-addsense.patch dpkg-source: info: applying gcc-7.patch dpkg-source: info: applying no_privacy_breach_url.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying no_enforcing_c++98.patch dpkg-source: info: applying gcc9.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 12 Jul 2026 01:47:37 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network sga_0.10.15-7 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network sga_0.10.15-7 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/sga-lJTTar/sga-0.10.15 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-fd935c1a-5d9e-4294-9472-17032a3dc410 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 sga dpkg-buildpackage: info: source version 0.10.15-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building sga using existing ../sga_0.10.15.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building sga in ../sga_0.10.15-7.debian.tar.xz dpkg-source: info: building sga in ../sga_0.10.15-7.dsc debian/rules binary dh binary --with python3 --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:7: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:24: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/general.m4:2976: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:689: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:696: AS_IF is expanded from... ./lib/autoconf/general.m4:2305: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2326: AC_CACHE_CHECK is expanded from... m4/m4_ax_openmp.m4:70: AX_OPENMP is expanded from... configure.ac:24: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:12: installing './compile' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Algorithm/Makefile.am: installing './depcomp' autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15' dh_auto_configure -- --with-bamtools=/usr/ cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/ checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether x86_64-linux-gnu-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-linux-gnu-g++... none checking for gcc... x86_64-linux-gnu-gcc checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-linux-gnu-gcc... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing clock_gettime... none required checking for OpenMP flag of C++ compiler... -fopenmp checking for host type... you are not using osx so multi-threading should work. checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for ext/hash_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for ext/hash_set... yes checking for api/BamReader.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15' dh_auto_build -O--sourcedirectory=src cd src && make -j2 make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' make all-recursive make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' Making all in bin make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/bin' cp -n sga-bam2de.pl sga-bam2de cp -n sga-mergeDriver.pl sga-mergeDriver make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/bin' Making all in Thirdparty make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o gzstream.o gzstream.C x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o stdaln.o stdaln.c x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o overlapper.o overlapper.cpp stdaln.c: In function ‘aln_local_core’: stdaln.c:756:17: warning: ‘free’ called on pointer ‘*(int **)((char *))’ with nonzero offset 4 [-Wfree-nonheap-object] 756 | free(s_array[i]); | ^~~~~~~~~~~~~~~~ overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers] 37 | OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers] 38 | OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers] x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o multiple_alignment.o multiple_alignment.cpp x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o bcr.o bcr.c bcr.c: In function ‘ld_restore’: bcr.c:183:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | fread(&ld->max, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:186:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 186 | fread(&x, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:189:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | fread(ld->a[i], 8, x, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o MurmurHash3.o MurmurHash3.cpp MurmurHash3.cpp: In function ‘void MurmurHash3_x86_32(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 132 | case 3: k1 ^= tail[2] << 16; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:133:3: note: here 133 | case 2: k1 ^= tail[1] << 8; | ^~~~ MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 133 | case 2: k1 ^= tail[1] << 8; | ~~~^~~~~~~~~~~~~~~ MurmurHash3.cpp:134:3: note: here 134 | case 1: k1 ^= tail[0]; | ^~~~ MurmurHash3.cpp: In function ‘void MurmurHash3_x86_128(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:207:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 207 | case 15: k4 ^= tail[14] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:208:3: note: here 208 | case 14: k4 ^= tail[13] << 8; | ^~~~ MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 208 | case 14: k4 ^= tail[13] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:209:3: note: here 209 | case 13: k4 ^= tail[12] << 0; | ^~~~ MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 210 | k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4; | ~~~^~~~~ MurmurHash3.cpp:212:3: note: here 212 | case 12: k3 ^= tail[11] << 24; | ^~~~ MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 212 | case 12: k3 ^= tail[11] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:213:3: note: here 213 | case 11: k3 ^= tail[10] << 16; | ^~~~ MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 213 | case 11: k3 ^= tail[10] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:214:3: note: here 214 | case 10: k3 ^= tail[ 9] << 8; | ^~~~ MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 214 | case 10: k3 ^= tail[ 9] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:215:3: note: here 215 | case 9: k3 ^= tail[ 8] << 0; | ^~~~ MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 216 | k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3; | ~~~^~~~~ MurmurHash3.cpp:218:3: note: here 218 | case 8: k2 ^= tail[ 7] << 24; | ^~~~ MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 218 | case 8: k2 ^= tail[ 7] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:219:3: note: here 219 | case 7: k2 ^= tail[ 6] << 16; | ^~~~ MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 219 | case 7: k2 ^= tail[ 6] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:220:3: note: here 220 | case 6: k2 ^= tail[ 5] << 8; | ^~~~ MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 220 | case 6: k2 ^= tail[ 5] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:221:3: note: here 221 | case 5: k2 ^= tail[ 4] << 0; | ^~~~ MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 222 | k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:224:3: note: here 224 | case 4: k1 ^= tail[ 3] << 24; | ^~~~ MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 224 | case 4: k1 ^= tail[ 3] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:225:3: note: here 225 | case 3: k1 ^= tail[ 2] << 16; | ^~~~ MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 225 | case 3: k1 ^= tail[ 2] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:226:3: note: here 226 | case 2: k1 ^= tail[ 1] << 8; | ^~~~ MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 226 | case 2: k1 ^= tail[ 1] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:227:3: note: here 227 | case 1: k1 ^= tail[ 0] << 0; | ^~~~ MurmurHash3.cpp: In function ‘void MurmurHash3_x64_128(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:296:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 296 | case 15: k2 ^= uint64_t(tail[14]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:297:3: note: here 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ^~~~ MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:298:3: note: here 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ^~~~ MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:299:3: note: here 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ^~~~ MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:300:3: note: here 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ^~~~ MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:301:3: note: here 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ^~~~ MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:302:3: note: here 302 | case 9: k2 ^= uint64_t(tail[ 8]) << 0; | ^~~~ MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 303 | k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:305:3: note: here 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ^~~~ MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:306:3: note: here 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ^~~~ MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:307:3: note: here 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ^~~~ MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:308:3: note: here 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ^~~~ MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:309:3: note: here 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ^~~~ MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:310:3: note: here 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ^~~~ MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:311:3: note: here 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ^~~~ MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:312:3: note: here 312 | case 1: k1 ^= uint64_t(tail[ 0]) << 0; | ^~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o count_min_sketch.o count_min_sketch.cpp rm -f libthirdparty.a ar cr libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ranlib libthirdparty.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' Making all in Util make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Util' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp In file included from Pileup.h:12, from Pileup.cpp:10: Pileup.cpp: In member function ‘DNADouble Pileup::calculateSimpleAlphaProb() const’: Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ Pileup.cpp:46:5: note: in expansion of macro ‘WARN_ONCE’ 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ Pileup.cpp:46:5: note: in expansion of macro ‘WARN_ONCE’ 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp rm -f libutil.a ar cr libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o ranlib libutil.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Util' Making all in SQG make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp rm -f libsqg.a ar cr libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ranlib libsqg.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' Making all in Bigraph make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp In file included from ../Util/EncodedString.h:22, from Vertex.h:23, from Vertex.cpp:9: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/15/bits/move.h:235:11: required from ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = EncodedString; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]’ 235 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ Vertex.cpp:46:18: required from here 46 | std::swap(m_seq, label); | ~~~~~~~~~^~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp rm -f libbigraph.a ar cr libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ranlib libbigraph.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' Making all in Algorithm make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp In file included from SearchHistory.h:12, from OverlapBlock.h:15, from OverlapBlock.cpp:11: OverlapBlock.cpp: In member function ‘std::string OverlapBlock::getFullString(const std::string&) const’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ OverlapBlock.cpp:88:9: note: in expansion of macro ‘WARN_ONCE’ 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ OverlapBlock.cpp:88:9: note: in expansion of macro ‘WARN_ONCE’ 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp In file included from ConnectProcess.cpp:10: ConnectProcess.h:10: warning: header guard ‘CONNECTROCESS_H’ followed by ‘#define’ of a different macro [-Wheader-guard] 10 | #ifndef CONNECTROCESS_H ConnectProcess.h:11: note: ‘CONNECTPROCESS_H’ is defined here; did you mean ‘CONNECTROCESS_H’? 11 | #define CONNECTPROCESS_H x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp rm -f libalgorithm.a ar cr libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ranlib libalgorithm.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' Making all in StringGraph make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from SGAlgorithms.h:13, from SGAlgorithms.cpp:9: SGAlgorithms.cpp: In function ‘Edge* SGAlgorithms::createEdgesFromOverlap(StringGraph*, const Overlap&, bool, size_t)’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ SGAlgorithms.cpp:60:9: note: in expansion of macro ‘WARN_ONCE’ 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ SGAlgorithms.cpp:60:9: note: in expansion of macro ‘WARN_ONCE’ 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp rm -f libstringgraph.a ar cr libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ranlib libstringgraph.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' Making all in Concurrency make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp rm -f libconcurrency.a ar cr libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ranlib libconcurrency.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' Making all in SuffixTools make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp In file included from STCommon.cpp:9: In member function ‘void SAElem::setID(uint64_t)’, inlined from ‘SAElem::SAElem(uint64_t)’ at STCommon.cpp:19:10: STCommon.h:53:13: warning: ‘*this.SAElem::m_val’ is used uninitialized [-Wuninitialized] 53 | m_val &= LOW_MASK; | ^~~~~ In member function ‘void SAElem::setID(uint64_t)’, inlined from ‘SAElem::SAElem(uint64_t, uint64_t)’ at STCommon.cpp:25:10: STCommon.h:53:13: warning: ‘*this.SAElem::m_val’ is used uninitialized [-Wuninitialized] 53 | m_val &= LOW_MASK; | ^~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp In file included from SuffixArray.cpp:10: InverseSuffixArray.h:10: warning: header guard ‘INVERSESUFFIXARRAY_H’ followed by ‘#define’ of a different macro [-Wheader-guard] 10 | #ifndef INVERSESUFFIXARRAY_H InverseSuffixArray.h:11: note: ‘INVERSESUFFIXARRAH_H’ is defined here; did you mean ‘INVERSESUFFIXARRAY_H’? 11 | #define INVERSESUFFIXARRAH_H x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp In file included from InverseSuffixArray.cpp:10: InverseSuffixArray.h:10: warning: header guard ‘INVERSESUFFIXARRAY_H’ followed by ‘#define’ of a different macro [-Wheader-guard] 10 | #ifndef INVERSESUFFIXARRAY_H InverseSuffixArray.h:11: note: ‘INVERSESUFFIXARRAH_H’ is defined here; did you mean ‘INVERSESUFFIXARRAY_H’? 11 | #define INVERSESUFFIXARRAH_H x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp In file included from ../Util/EncodedString.h:22, from Occurrence.h:13, from RLBWT.h:13, from BWT.h:18, from BWTDiskConstruction.h:19, from BWTDiskConstruction.cpp:12: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/15/bits/new_allocator.h:191:4: required from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]’ 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/alloc_traits.h:674:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]’ 674 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/vector.tcc:117:30: required from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]’ 117 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_vector.h:1434:21: required from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]’ 1434 | { emplace_back(std::move(__x)); } | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ BWTDiskConstruction.cpp:252:36: required from here 252 | readSequences.push_back(item.seq.toString()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp rm -f libsuffixtools.a ar cr libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ranlib libsuffixtools.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' Making all in Scaffold make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: ScaffoldGroup.cpp: In member function ‘void ScaffoldGroup::getSecondaryLinks()’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ ScaffoldGroup.cpp:279:13: note: in expansion of macro ‘WARN_ONCE’ 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ ScaffoldGroup.cpp:279:13: note: in expansion of macro ‘WARN_ONCE’ 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp rm -f libscaffold.a ar cr libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ranlib libscaffold.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' Making all in GraphDiff make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp DindelUtil.cpp: In function ‘DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)’: DindelUtil.cpp:65:10: warning: variable ‘has_complex_variant’ set but not used [-Wunused-but-set-variable] 65 | bool has_complex_variant = false; | ^~~~~~~~~~~~~~~~~~~ DindelRealignWindow.cpp: In member function ‘void DindelHaplotype::write(std::ostream&) const’: DindelRealignWindow.cpp:762:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 762 | for (size_t x=0; x::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelRealignWindow.cpp:1037:115: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1037 | for (std::list::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector&, std::unordered_map, std::__cxx11::list >&, const std::vector >&)’: DindelRealignWindow.cpp:2589:12: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2589 | for (int h1=0;h1&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2743:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2743 | for (size_t x=0;x&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2906:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2906 | for (size_t x=0;x::pair(_U1&&, _U2&&) [with _U1 = int&; _U2 = DindelRealignWindowResult::Inference; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = const int; _T2 = DindelRealignWindowResult::Inference]’ at /usr/include/c++/15/bits/stl_pair.h:902:35, inlined from ‘void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)’ at DindelRealignWindow.cpp:2633:228: DindelRealignWindow.h:637:15: warning: ‘.DindelRealignWindowResult::Inference::qual’ is used uninitialized [-Wuninitialized] 637 | class Inference | ^~~~~~~~~ DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2633:227: note: ‘’ declared here 2633 | std::pair hapit_pair = result.hapIdxToInference.insert(DindelRealignWindowResult::HapIdxToInference::value_type(hapIdx,DindelRealignWindowResult::Inference())); | ^ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp In constructor ‘DindelRealignWindowResult::Inference::Inference(DindelRealignWindowResult::Inference&&)’, inlined from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = int&; _U2 = DindelRealignWindowResult::Inference; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = const int; _T2 = DindelRealignWindowResult::Inference]’ at /usr/include/c++/15/bits/stl_pair.h:902:35, inlined from ‘void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)’ at DindelRealignWindow.cpp:2774:147: DindelRealignWindow.h:637:15: warning: ‘.DindelRealignWindowResult::Inference::qual’ is used uninitialized [-Wuninitialized] 637 | class Inference | ^~~~~~~~~ DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2774:146: note: ‘’ declared here 2774 | result.hapIdxToInference.insert(DindelRealignWindowResult::HapIdxToInference::value_type(hapIdx,DindelRealignWindowResult::Inference())); | ^ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp DeBruijnHaplotypeBuilder.cpp: In member function ‘Vertex* DeBruijnHaplotypeBuilder::extendUnambiguously(Vertex*, StringGraph*, EdgeDir, size_t, size_t)’: DeBruijnHaplotypeBuilder.cpp:227:16: warning: variable ‘ext_count’ set but not used [-Wunused-but-set-variable] 227 | size_t ext_count = 0; | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp rm -f libgraphdiff.a ar cr libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o ranlib libgraphdiff.a make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' Making all in SGA make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp In file included from ../Util/EncodedString.h:22, from ../SuffixTools/Occurrence.h:13, from ../SuffixTools/RLBWT.h:13, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTDiskConstruction.h:19, from index.cpp:18: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ 43 | _copy(other); | ~~~~~^~~~~~~ /usr/include/c++/15/bits/new_allocator.h:191:4: required from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]’ 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/alloc_traits.h:674:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]’ 674 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/vector.tcc:117:30: required from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]’ 117 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_vector.h:1434:21: required from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]’ 1434 | { emplace_back(std::move(__x)); } | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ index.cpp:130:27: required from here 130 | readSequences.push_back(sr.seq.toString()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp In file included from connect.cpp:26: ../Algorithm/ConnectProcess.h:10: warning: header guard ‘CONNECTROCESS_H’ followed by ‘#define’ of a different macro [-Wheader-guard] 10 | #ifndef CONNECTROCESS_H ../Algorithm/ConnectProcess.h:11: note: ‘CONNECTPROCESS_H’ is defined here; did you mean ‘CONNECTROCESS_H’? 11 | #define CONNECTPROCESS_H x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp In file included from connect.cpp:15: connect.cpp: In function ‘int connectMain(int, char**)’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ connect.cpp:297:17: note: in expansion of macro ‘WARN_ONCE’ 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ connect.cpp:297:17: note: in expansion of macro ‘WARN_ONCE’ 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp In file included from filterBAM.cpp:25: ../Algorithm/ConnectProcess.h:10: warning: header guard ‘CONNECTROCESS_H’ followed by ‘#define’ of a different macro [-Wheader-guard] 10 | #ifndef CONNECTROCESS_H ../Algorithm/ConnectProcess.h:11: note: ‘CONNECTPROCESS_H’ is defined here; did you mean ‘CONNECTROCESS_H’? 11 | #define CONNECTPROCESS_H x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp graph-concordance.cpp: In function ‘std::string reconstructHaplotype(const VCFRecord&, VariantRecordVector, const ReadTable&, const BWTIndexSet&, size_t)’: graph-concordance.cpp:214:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 214 | if(end > chr.seq.length()) | ~~~~^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp In file included from ../Thirdparty/rapidjson/reader.h:7, from ../Thirdparty/rapidjson/document.h:4, from preqc.cpp:27: ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF8::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef170’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:170:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 170 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static rapidjson::UTF8::Ch rapidjson::UTF8::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef183’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:183:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 183 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef189’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:189:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 189 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8::Put(OutputByteStream&, Ch)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef195’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:195:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 195 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16::Encode(OutputStream&, unsigned int)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef219’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:219:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 219 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16::Decode(InputStream&, unsigned int*)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef234’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:234:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 234 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16::Validate(InputStream&, OutputStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef252’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:252:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 252 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef253’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:253:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 253 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef271’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:271:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 271 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef278’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:278:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 278 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef286’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:286:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 286 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef292’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:292:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 292 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef303’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:303:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 303 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef310’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:310:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 310 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef318’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:318:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 318 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef324’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:324:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 324 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32::Encode(OutputStream&, unsigned int)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef348’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:348:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 348 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32::Decode(InputStream&, unsigned int*)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef355’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:355:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 355 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32::Validate(InputStream&, OutputStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef363’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:363:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 363 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef375’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:375:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 375 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef382’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:382:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 382 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef392’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:392:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 392 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef398’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:398:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 398 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef411’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:411:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 411 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef418’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:418:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 418 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef428’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:428:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 428 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef434’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:434:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 434 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp somatic-variant-filters.cpp: In function ‘CoverageStats getVariantCoverage(BamTools::BamReader*, const VCFRecord&, const ReadTable*)’: somatic-variant-filters.cpp:305:24: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 305 | std::random_shuffle(alignments.begin(), alignments.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from somatic-variant-filters.cpp:16: /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function ‘std::vector simulateCoverageHaploid(double, size_t, size_t)’: haplotype-filter.cpp:722:24: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 722 | std::random_shuffle(indices.begin(), indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from haplotype-filter.cpp:16: /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function ‘std::vector simulateCoverageDiploid(double, size_t, size_t)’: haplotype-filter.cpp:756:24: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 756 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function ‘std::vector simulateCoverageHaploidNonUniform(std::vector, size_t, double&)’: haplotype-filter.cpp:837:24: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 837 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ haplotype-filter.cpp: In function ‘std::vector simulateCoverageDiploidNonUniform(std::vector, size_t, double&)’: haplotype-filter.cpp:903:24: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 903 | std::random_shuffle(initial_indices.begin(), initial_indices.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp x86_64-linux-gnu-g++ -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-lJTTar/sga-0.10.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -L/usr//lib -L/usr//lib/bamtools -Wl,-z,relro -Wl,-z,now -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lz -lbamtools make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' dh_auto_test -O--sourcedirectory=src cd src && make -j2 check TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' Making check in bin make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/bin' Making check in Thirdparty make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' Making check in Util make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Util' Making check in SQG make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' Making check in Bigraph make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' Making check in Algorithm make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' Making check in StringGraph make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' Making check in Concurrency make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' Making check in SuffixTools make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' Making check in Scaffold make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' Making check in GraphDiff make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' Making check in SGA make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15' dh_auto_install cd src && make -j2 install DESTDIR=/build/sga-lJTTar/sga-0.10.15/debian/sga AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' Making install in bin make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/bin' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/bin' /usr/bin/mkdir -p '/build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c sga-bam2de sga-mergeDriver '/build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/bin' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/bin' Making install in Thirdparty make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Thirdparty' Making install in Util make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Util' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Util' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Util' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Util' Making install in SQG make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SQG' Making install in Bigraph make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Bigraph' Making install in Algorithm make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Algorithm' Making install in StringGraph make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/StringGraph' Making install in Concurrency make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Concurrency' Making install in SuffixTools make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SuffixTools' Making install in Scaffold make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/Scaffold' Making install in GraphDiff make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/GraphDiff' Making install in SGA make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin' /usr/bin/install -c sga '/build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' make[4]: Entering directory '/build/sga-lJTTar/sga-0.10.15/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' make[3]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-lJTTar/sga-0.10.15/src' cp -a src/bin/sga-bam2de.pl debian/sga/usr/bin/sga-bam2de cp -a src/bin/sga-astat.py debian/sga/usr/bin/sga-astat make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15' dh_installexamples mkdir -p debian/sga/usr/share/doc/sga/examples sed -e 's?^\(SGA_BIN=sga\).*?\1?' \ -e 's?^.*/bin/sga-align?sga-align?' \ -e 's?^.*/bin/sga-bam2de.pl?sga-bam2de?' \ -e 's?^.*/bin/sga-astat.py?sga-astat?' \ src/examples/sga-celegans.sh > debian/sga/usr/share/doc/sga/examples/sga-celegans.sh make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15' debian/rules override_dh_installman make[1]: Entering directory '/build/sga-lJTTar/sga-0.10.15' dh_installman mkdir -p /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/share/man/man1/ PATH=/usr/lib/abyss:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man \ --version-string="0.10.15" \ --no-info \ --name "Make a distance estimate file from a bam file of reads aligned to contigs" \ --output /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/share/man/man1//sga-bam2de.1 \ /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin/sga-bam2de help2man \ --no-info \ --version-string="0.10.15" \ --name="String Graph Assembler: de novo genome assembler that uses string graphs" \ --output /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/share/man/man1//sga.1 \ /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin/sga help2man \ --no-info\ --version-string="0.10.15" \ --name="generate sga merge commands from a list of files" \ --output /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/share/man/man1//sga-mergeDriver.1 \ /build/sga-lJTTar/sga-0.10.15/debian/sga/usr/bin/sga-mergeDriver make[1]: Leaving directory '/build/sga-lJTTar/sga-0.10.15' dh_python3 -O--sourcedirectory=src I: dh_python3 tools:129: replacing shebang in debian/sga/usr/bin/sga-align I: dh_python3 tools:129: replacing shebang in debian/sga/usr/bin/sga-astat dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-7_amd64.deb'. dpkg-deb: building package 'sga' in '../sga_0.10.15-7_amd64.deb'. dpkg-genbuildinfo -O../sga_0.10.15-7_amd64.buildinfo dpkg-genchanges -O../sga_0.10.15-7_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 2026-07-12T01:50:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 12 Jul 2026 01:50:58 +0000 | +------------------------------------------------------------------------------+ sga_0.10.15-7_amd64.changes: ---------------------------- Format: 1.8 Date: Fri, 17 Sep 2021 15:56:21 +0200 Source: sga Binary: sga sga-dbgsym Architecture: source amd64 Version: 0.10.15-7 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: sga - de novo genome assembler that uses string graphs Changes: sga (0.10.15-7) unstable; urgency=medium . * Fix watchfile to detect new versions on github (routine-update) * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Include ${perl:Depends} Checksums-Sha1: 7c49d66a6349f47adf50c978532dacd16a7460f7 1201 sga_0.10.15-7.dsc 5e2ac042aba7b7313171220d65b600ec4279b98f 214364 sga_0.10.15-7.debian.tar.xz 71166f2881283bb0ca8960a19262f60de79ab5ca 15593416 sga-dbgsym_0.10.15-7_amd64.deb 806b42af12a50966a79079d6840116f451d5fa4a 8474 sga_0.10.15-7_amd64.buildinfo 18fff16d841d6caff49f977bb87f6149cdb65e30 885292 sga_0.10.15-7_amd64.deb Checksums-Sha256: 6f1b52003edab1c72f31a3c1eeccc7cf024b804832fa3b044f13122dedca7391 1201 sga_0.10.15-7.dsc 01b6066d6287df0b83b4ca0c3014ff5f9687dc77301c5b2a194e50624b19d000 214364 sga_0.10.15-7.debian.tar.xz b0ae72cf0826922cea143d5c22204e6fe13e7427d7cde2c809d85139ccf410fa 15593416 sga-dbgsym_0.10.15-7_amd64.deb e63387c1bd9f27ac3920bce1679d6453fc57765c30c6c71f5d801a51405c2a66 8474 sga_0.10.15-7_amd64.buildinfo c8922276dffec0f14a7b3d22fd84e4d8a5db22e6118162b559a25881fc4ccb02 885292 sga_0.10.15-7_amd64.deb Files: d85147d75739dba8627115e5115b6b03 1201 science optional sga_0.10.15-7.dsc ba95cf535d152cfc1c290702feff09c8 214364 science optional sga_0.10.15-7.debian.tar.xz 8df3b7ab38f755f208787a7151ec21b4 15593416 debug optional sga-dbgsym_0.10.15-7_amd64.deb 6be67c6c21fae8c221adb05b192cce58 8474 science optional sga_0.10.15-7_amd64.buildinfo ecb49ea61a29538475072fc90bf81354 885292 science optional sga_0.10.15-7_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 12 Jul 2026 01:50:58 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: sga Binary: sga sga-dbgsym Architecture: amd64 source Version: 0.10.15-7 Checksums-Md5: d85147d75739dba8627115e5115b6b03 1201 sga_0.10.15-7.dsc 8df3b7ab38f755f208787a7151ec21b4 15593416 sga-dbgsym_0.10.15-7_amd64.deb ecb49ea61a29538475072fc90bf81354 885292 sga_0.10.15-7_amd64.deb Checksums-Sha1: 7c49d66a6349f47adf50c978532dacd16a7460f7 1201 sga_0.10.15-7.dsc 71166f2881283bb0ca8960a19262f60de79ab5ca 15593416 sga-dbgsym_0.10.15-7_amd64.deb 18fff16d841d6caff49f977bb87f6149cdb65e30 885292 sga_0.10.15-7_amd64.deb Checksums-Sha256: 6f1b52003edab1c72f31a3c1eeccc7cf024b804832fa3b044f13122dedca7391 1201 sga_0.10.15-7.dsc b0ae72cf0826922cea143d5c22204e6fe13e7427d7cde2c809d85139ccf410fa 15593416 sga-dbgsym_0.10.15-7_amd64.deb c8922276dffec0f14a7b3d22fd84e4d8a5db22e6118162b559a25881fc4ccb02 885292 sga_0.10.15-7_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 12 Jul 2026 01:50:57 +0000 Build-Path: /build/sga-lJTTar/sga-0.10.15 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-python (= 7.20260623), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), fontconfig (= 2.17.1-5), fontconfig-config (= 2.17.1-5), fonts-dejavu-core (= 2.37-9), fonts-dejavu-mono (= 2.37-9), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), graphviz (= 14.1.2-1+b3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libabsl20260107 (= 20260107.0-5), libacl1 (= 2.4.0-1), libaom3 (= 3.13.1-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libavif16 (= 1.4.2-1), libbamtools-dev (= 2.5.3+dfsg-2), libbamtools2.5.3 (= 2.5.3+dfsg-2), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcairo2 (= 1.18.4-3+b1), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcdt6 (= 14.1.2-1+b3), libcgraph8 (= 14.1.2-1+b3), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-2), libcurl4-gnutls (= 8.21.0-2), libdatrie1 (= 0.2.14-2), libdav1d7 (= 1.5.3-1+b2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libde265-0 (= 1.1.1-1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libexpat1 (= 2.8.2-1), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libfontconfig1 (= 2.17.1-5), libfreetype6 (= 2.14.3+dfsg-1), libfribidi0 (= 1.0.16-5+b1), libgav1-2 (= 0.20.0-2+b1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgd3 (= 2.3.3-13+b2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libglib2.0-0t64 (= 2.88.2-1), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgraphite2-3 (= 1.3.15-2), libgssapi-krb5-2 (= 1.22.1-3), libgvc7 (= 14.1.2-1+b3), libgvplugin-gd8 (= 14.1.2-1+b3), libgvplugin-pango8 (= 14.1.2-1+b3), libgvpr2 (= 14.1.2-1+b3), libharfbuzz0b (= 12.3.2-2+b2), libheif-plugin-dav1d (= 1.23.1-1), libheif-plugin-libde265 (= 1.23.1-1), libheif1 (= 1.23.1-1), libhogweed6t64 (= 3.10.2-1+b1), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libimagequant0 (= 4.4.1-1+b2), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libjbig0 (= 2.1-6.1+b3), libjpeg62-turbo (= 1:3.1.3-4), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap2 (= 2.6.13+dfsg-1+b1), liblerc4 (= 4.1.1+ds-1), liblocale-gettext-perl (= 1.07-10+b1), liblsan0 (= 16.1.0-2), libltdl7 (= 2.5.4-11), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncurses6 (= 6.6+20260608-2), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libp11-kit0 (= 0.26.4-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpango-1.0-0 (= 1.58.0-1), libpangocairo-1.0-0 (= 1.58.0-1), libpangoft2-1.0-0 (= 1.58.0-1), libpathplan4 (= 14.1.2-1+b3), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpixman-1-0 (= 0.46.4-1+b2), libpng16-16t64 (= 1.6.58-1), libpsl5t64 (= 0.22.0-1), libpython3-stdlib (= 3.14.6-1), libpython3.14-minimal (= 3.14.6-1), libpython3.14-stdlib (= 3.14.6-1), libquadmath0 (= 16.1.0-2), librav1e0.8 (= 0.8.1-10), libreadline8t64 (= 8.3-4), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libsharpyuv0 (= 1.5.0-0.1+b2), libsmartcols1 (= 2.42.2-1), libsparsehash-dev (= 2.0.4-1), libsqlite3-0 (= 3.53.3-1), libssh2-1t64 (= 1.11.1-4), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsvtav1enc4 (= 4.1.0+dfsg-1), libsystemd0 (= 261.1-2), libtasn1-6 (= 4.21.0-2+b1), libthai-data (= 0.1.30-2), libthai0 (= 0.1.30-2), libtiff6 (= 4.7.2-1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libwebp7 (= 1.5.0-0.1+b2), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb-render0 (= 1.17.0-2+b2), libxcb-shm0 (= 1.17.0-2+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxdot4 (= 14.1.2-1+b3), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxpm4 (= 1:3.5.19-1), libxrender1 (= 1:0.9.12-1+b2), libyuv0 (= 0.0.1949.20260706-1), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), netbase (= 6.5), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), po-debconf (= 1.0.22), python3 (= 3.14.6-1), python3-minimal (= 3.14.6-1), python3-pysam (= 0.23.3+ds-2+b1), python3-ruffus (= 2.8.4-8), python3.14 (= 3.14.6-1), python3.14-minimal (= 3.14.6-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.4-1), samtools (= 1.22.1-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tzdata (= 2026b-1), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1631886981" +------------------------------------------------------------------------------+ | Package contents Sun, 12 Jul 2026 01:50:58 +0000 | +------------------------------------------------------------------------------+ sga-dbgsym_0.10.15-7_amd64.deb ------------------------------ new Debian package, version 2.0. size 15593416 bytes: control archive=532 bytes. 360 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: sga-dbgsym Source: sga Version: 0.10.15-7 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 16096 Depends: sga (= 0.10.15-7) Section: debug Priority: optional Description: debug symbols for sga Build-Ids: a755d363665e12c4fd13a0a26f813ffa8140ced5 drwxr-xr-x root/root 0 2021-09-17 13:56 ./ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/lib/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/lib/debug/.build-id/a7/ -rw-r--r-- root/root 16471592 2021-09-17 13:56 ./usr/lib/debug/.build-id/a7/55d363665e12c4fd13a0a26f813ffa8140ced5.debug drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-09-17 13:56 ./usr/share/doc/sga-dbgsym -> sga sga_0.10.15-7_amd64.deb ----------------------- new Debian package, version 2.0. size 885292 bytes: control archive=1268 bytes. 868 bytes, 17 lines control 1066 bytes, 17 lines md5sums Package: sga Version: 0.10.15-7 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2574 Depends: libbamtools2.5.3 (>= 2.5.3+dfsg), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 14), zlib1g (>= 1:1.1.4), python3:any, perl:any, samtools, python3-ruffus, python3-pysam Recommends: abyss Section: science Priority: optional Homepage: https://github.com/jts/sga Description: de novo genome assembler that uses string graphs The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. . SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. drwxr-xr-x root/root 0 2021-09-17 13:56 ./ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/bin/ -rwxr-xr-x root/root 2582792 2021-09-17 13:56 ./usr/bin/sga -rwxr-xr-x root/root 4509 2021-09-17 13:56 ./usr/bin/sga-align -rwxr-xr-x root/root 5735 2021-09-17 13:56 ./usr/bin/sga-astat -rwxr-xr-x root/root 3290 2021-09-17 13:56 ./usr/bin/sga-bam2de -rwxr-xr-x root/root 1873 2021-09-17 13:56 ./usr/bin/sga-mergeDriver drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/doc/sga/ -rw-r--r-- root/root 349 2021-09-17 13:53 ./usr/share/doc/sga/README.Debian -rw-r--r-- root/root 3280 2016-08-05 20:27 ./usr/share/doc/sga/README.gz -rw-r--r-- root/root 515 2016-08-05 20:27 ./usr/share/doc/sga/README.md -rw-r--r-- root/root 839 2021-09-17 13:56 ./usr/share/doc/sga/changelog.Debian.gz -rw-r--r-- root/root 3396 2021-09-17 13:53 ./usr/share/doc/sga/copyright drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/doc/sga/examples/ -rw-r--r-- root/root 3312 2021-09-17 13:56 ./usr/share/doc/sga/examples/sga-celegans.sh -rw-r--r-- root/root 3391 2021-09-17 13:56 ./usr/share/doc/sga/index.html drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/man/ drwxr-xr-x root/root 0 2021-09-17 13:56 ./usr/share/man/man1/ -rw-r--r-- root/root 517 2021-09-17 13:56 ./usr/share/man/man1/sga-align.1.gz -rw-r--r-- root/root 656 2021-09-17 13:56 ./usr/share/man/man1/sga-astat.1.gz -rw-r--r-- root/root 522 2021-09-17 13:56 ./usr/share/man/man1/sga-bam2de.1.gz -rw-r--r-- root/root 328 2021-09-17 13:56 ./usr/share/man/man1/sga-mergeDriver.1.gz -rw-r--r-- root/root 1024 2021-09-17 13:56 ./usr/share/man/man1/sga.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 12 Jul 2026 01:50:58 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 12 Jul 2026 01:50:58 +0000 | +------------------------------------------------------------------------------+ Purging /build/sga-lJTTar Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 12 Jul 2026 01:50:59 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 397200 Build-Time: 200 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 22 Job: /srv/debomatic/incoming/sga_0.10.15-7.dsc Machine Architecture: amd64 Package: sga Package-Time: 233 Source-Version: 0.10.15-7 Space: 397200 Status: successful Version: 0.10.15-7 -------------------------------------------------------------------------------- Finished at 2026-07-12T01:50:57Z Build needed 00:03:53, 397200k disk space