sbuild (Debian sbuild) 0.78.1 (09 February 2019) on carme.larted.org.uk +====================================================================================+ | gatb-core 1.4.1+git20181225.44d5a44+dfsg-2 (amd64) Fri, 07 Jun 2019 23:15:47 +0000 | +====================================================================================+ Package: gatb-core Version: 1.4.1+git20181225.44d5a44+dfsg-2 Source Version: 1.4.1+git20181225.44d5a44+dfsg-2 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-e31d126c-d274-4817-86bb-79360b7cf74a' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gatb-core_1.4.1+git20181225.44d5a44+dfsg-2 sid amd64 --------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gatb-core_1.4.1+git20181225.44d5a44+dfsg-2 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/gatb-core-GOnGmq/resolver-2bdAhe' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [210 kB] Get:2 http://localhost:3142/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main Sources 2019-06-07-0304.14.pdiff [4374 B] Get:5 http://localhost:3142/debian unstable/main Sources 2019-06-07-0813.19.pdiff [262 B] Get:6 http://localhost:3142/debian unstable/main Sources 2019-06-07-1432.00.pdiff [3406 B] Get:7 http://localhost:3142/debian unstable/main Sources 2019-06-07-2014.58.pdiff [425 B] Get:8 http://localhost:3142/debian unstable/main amd64 Packages 2019-06-07-0304.14.pdiff [855 B] Get:9 http://localhost:3142/debian unstable/main amd64 Packages 2019-06-07-0813.19.pdiff [6852 B] Get:10 http://localhost:3142/debian unstable/main amd64 Packages 2019-06-07-1432.00.pdiff [5724 B] Get:11 http://localhost:3142/debian unstable/main amd64 Packages 2019-06-07-2014.58.pdiff [2676 B] Get:7 http://localhost:3142/debian unstable/main Sources 2019-06-07-2014.58.pdiff [425 B] Get:11 http://localhost:3142/debian unstable/main amd64 Packages 2019-06-07-2014.58.pdiff [2676 B] Fetched 290 kB in 2s (160 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/gatb-core-GOnGmq/gatb-core-1.4.1+git20181225.44d5a44+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gatb-core-GOnGmq' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 12~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [422 B] Get:5 copy:/<>/apt_archive ./ Packages [502 B] Fetched 1881 B in 0s (38.2 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... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz fakeroot file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.67-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhdf5-103 libhdf5-cpp-103 libhdf5-dev libice6 libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 libllvm6.0 libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 librhash0 librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1 libsz2 libthai-data libthai0 libtiff5 libtool libuchardet0 libuv1 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf procps sensible-utils ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff lrzip libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev libcppunit-doc libgd-tools krb5-doc krb5-user libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx fonts-liberation ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz fakeroot file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.67-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhdf5-103 libhdf5-cpp-103 libhdf5-dev libice6 libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblab-gamut1 libllvm6.0 libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libprocps7 libpsl5 librhash0 librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1 libsz2 libthai-data libthai0 libtiff5 libtool libuchardet0 libuv1 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf procps sbuild-build-depends-main-dummy sensible-utils ucf x11-common zlib1g-dev 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 80.8 MB of archives. After this operation, 398 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:2 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://localhost:3142/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:10 http://localhost:3142/debian unstable/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:11 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:14 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:15 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:16 http://localhost:3142/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:18 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:19 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:20 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:21 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:22 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:23 http://localhost:3142/debian unstable/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libarchive13 amd64 3.3.3-4 [314 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.17-2 [65.6 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.17-2 [121 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.17-2 [368 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-2 [158 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.37.0-1 [83.3 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:35 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libcurl4 amd64 7.64.0-3 [331 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:40 http://localhost:3142/debian unstable/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get:42 http://localhost:3142/debian unstable/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get:43 http://localhost:3142/debian unstable/main amd64 d-shlibs all 0.84 [17.2 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:45 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:48 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:50 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-2 [1259 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:53 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:54 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:55 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:56 http://localhost:3142/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libllvm6.0 amd64 1:6.0.1-11 [14.8 MB] Get:59 http://localhost:3142/debian unstable/main amd64 libclang1-6.0 amd64 1:6.0.1-11 [7065 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libxapian30 amd64 1.4.11-1 [1104 kB] Get:61 http://localhost:3142/debian unstable/main amd64 doxygen amd64 1.8.13-10 [3985 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.23-1 [45.9 kB] Get:63 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.23-1 [85.8 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:66 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:67 http://localhost:3142/debian unstable/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:69 http://localhost:3142/debian unstable/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libcdt5 amd64 2.40.1-6 [60.6 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libcgraph6 amd64 2.40.1-6 [84.1 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libtiff5 amd64 4.0.10-4 [257 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libgd3 amd64 2.2.5-5.1 [136 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.6-10 [390 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libfribidi0 amd64 1.0.5-3.1 [63.5 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libthai-data all 0.1.28-2 [170 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libpango-1.0-0 amd64 1.42.4-6 [185 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.42.4-6 [67.9 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.42.4-6 [55.5 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libpathplan4 amd64 2.40.1-6 [63.5 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libxdot4 amd64 2.40.1-6 [56.9 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libgvc6 amd64 2.40.1-6 [646 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libgvpr2 amd64 2.40.1-6 [213 kB] Get:104 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:106 http://localhost:3142/debian unstable/main amd64 liblab-gamut1 amd64 2.40.1-6 [220 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:111 http://localhost:3142/debian unstable/main amd64 graphviz amd64 2.40.1-6 [594 kB] Get:112 http://localhost:3142/debian unstable/main amd64 hdf5-helpers amd64 1.10.4+repack-10 [35.2 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:115 http://localhost:3142/debian unstable/main amd64 libaec-dev amd64 1.0.2-1 [18.4 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libboost1.67-dev amd64 1.67.0-13 [8386 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get:118 http://localhost:3142/debian unstable/main amd64 libcppunit-1.14-0 amd64 1.14.0-3 [140 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libcppunit-dev amd64 1.14.0-3 [196 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 8.3.0-7 [581 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libhdf5-cpp-103 amd64 1.10.4+repack-10 [146 kB] Get:123 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:1.5.2-2+b1 [208 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libjpeg-dev all 1:1.5.2-2 [57.5 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libhdf5-dev amd64 1.10.4+repack-10 [2598 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libjsoncpp-dev amd64 1.7.4-3 [86.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.8 MB in 1s (84.6 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15123 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../006-libncurses6_6.1+20181013-2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../007-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package procps. Preparing to unpack .../008-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../009-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../010-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../011-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../012-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../013-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../015-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package cmake-data. Preparing to unpack .../021-cmake-data_3.13.4-1_all.deb ... Unpacking cmake-data (3.13.4-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../022-libicu63_63.1-6_amd64.deb ... Unpacking libicu63:amd64 (63.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../023-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../024-libarchive13_3.3.3-4_amd64.deb ... Unpacking libarchive13:amd64 (3.3.3-4) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../025-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../026-libkrb5support0_1.17-2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../027-libk5crypto3_1.17-2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../028-libssl1.1_1.1.1c-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1c-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../029-libkrb5-3_1.17-2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-2) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../030-libgssapi-krb5-2_1.17-2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../031-libnghttp2-14_1.37.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.37.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../032-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../034-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../035-libcurl4_7.64.0-3_amd64.deb ... Unpacking libcurl4:amd64 (7.64.0-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../036-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../037-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../038-librhash0_1.3.8-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.8-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../039-libuv1_1.24.1-1_amd64.deb ... Unpacking libuv1:amd64 (1.24.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.13.4-1_amd64.deb ... Unpacking cmake (3.13.4-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../041-d-shlibs_0.84_all.deb ... Unpacking d-shlibs (0.84) ... Selecting previously unselected package libtool. Preparing to unpack .../042-libtool_2.4.6-10_all.deb ... Unpacking libtool (2.4.6-10) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../043-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../044-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../045-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../046-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../047-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../048-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../049-libglib2.0-0_2.58.3-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../050-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../053-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../055-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm6.0:amd64. Preparing to unpack .../056-libllvm6.0_1%3a6.0.1-11_amd64.deb ... Unpacking libllvm6.0:amd64 (1:6.0.1-11) ... Selecting previously unselected package libclang1-6.0. Preparing to unpack .../057-libclang1-6.0_1%3a6.0.1-11_amd64.deb ... Unpacking libclang1-6.0 (1:6.0.1-11) ... Selecting previously unselected package libxapian30:amd64. Preparing to unpack .../058-libxapian30_1.4.11-1_amd64.deb ... Unpacking libxapian30:amd64 (1.4.11-1) ... Selecting previously unselected package doxygen. Preparing to unpack .../059-doxygen_1.8.13-10_amd64.deb ... Unpacking doxygen (1.8.13-10) ... Selecting previously unselected package libfakeroot:amd64. Preparing to unpack .../060-libfakeroot_1.23-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.23-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../061-fakeroot_1.23-1_amd64.deb ... Unpacking fakeroot (1.23-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../062-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../063-libfreetype6_2.9.1-3_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../064-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../065-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../066-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../067-fontconfig_2.13.1-2_amd64.deb ... Unpacking fontconfig (2.13.1-2) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../068-libpixman-1-0_0.36.0-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.36.0-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../069-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../071-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../073-libx11-6_2%3a1.6.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../074-libxcb-render0_1.13.1-2_amd64.deb ... Unpacking libxcb-render0:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../075-libxcb-shm0_1.13.1-2_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.13.1-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../076-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../077-libxrender1_1%3a0.9.10-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../078-libcairo2_1.16.0-4_amd64.deb ... Unpacking libcairo2:amd64 (1.16.0-4) ... Selecting previously unselected package libcdt5. Preparing to unpack .../079-libcdt5_2.40.1-6_amd64.deb ... Unpacking libcdt5 (2.40.1-6) ... Selecting previously unselected package libcgraph6. Preparing to unpack .../080-libcgraph6_2.40.1-6_amd64.deb ... Unpacking libcgraph6 (2.40.1-6) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../081-libjpeg62-turbo_1%3a1.5.2-2+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../082-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../083-libwebp6_0.6.1-2_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../084-libtiff5_4.0.10-4_amd64.deb ... Unpacking libtiff5:amd64 (4.0.10-4) ... Selecting previously unselected package libxpm4:amd64. Preparing to unpack .../085-libxpm4_1%3a3.5.12-1_amd64.deb ... Unpacking libxpm4:amd64 (1:3.5.12-1) ... Selecting previously unselected package libgd3:amd64. Preparing to unpack .../086-libgd3_2.2.5-5.1_amd64.deb ... Unpacking libgd3:amd64 (2.2.5-5.1) ... Selecting previously unselected package libgts-0.7-5:amd64. Preparing to unpack .../087-libgts-0.7-5_0.7.6+darcs121130-4_amd64.deb ... Unpacking libgts-0.7-5:amd64 (0.7.6+darcs121130-4) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../088-libltdl7_2.4.6-10_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-10) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../089-libfribidi0_1.0.5-3.1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.5-3.1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../090-libthai-data_0.1.28-2_all.deb ... Unpacking libthai-data (0.1.28-2) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../091-libdatrie1_0.2.12-2_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.12-2) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../092-libthai0_0.1.28-2_amd64.deb ... Unpacking libthai0:amd64 (0.1.28-2) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../093-libpango-1.0-0_1.42.4-6_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.42.4-6) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../094-libgraphite2-3_1.3.13-7_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.13-7) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../095-libharfbuzz0b_2.3.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (2.3.1-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../096-libpangoft2-1.0-0_1.42.4-6_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.42.4-6) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../097-libpangocairo-1.0-0_1.42.4-6_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.42.4-6) ... Selecting previously unselected package libpathplan4. Preparing to unpack .../098-libpathplan4_2.40.1-6_amd64.deb ... Unpacking libpathplan4 (2.40.1-6) ... Selecting previously unselected package libxdot4. Preparing to unpack .../099-libxdot4_2.40.1-6_amd64.deb ... Unpacking libxdot4 (2.40.1-6) ... Selecting previously unselected package libgvc6. Preparing to unpack .../100-libgvc6_2.40.1-6_amd64.deb ... Unpacking libgvc6 (2.40.1-6) ... Selecting previously unselected package libgvpr2. Preparing to unpack .../101-libgvpr2_2.40.1-6_amd64.deb ... Unpacking libgvpr2 (2.40.1-6) ... Selecting previously unselected package x11-common. Preparing to unpack .../102-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../103-libice6_2%3a1.0.9-2_amd64.deb ... Unpacking libice6:amd64 (2:1.0.9-2) ... Selecting previously unselected package liblab-gamut1. Preparing to unpack .../104-liblab-gamut1_2.40.1-6_amd64.deb ... Unpacking liblab-gamut1 (2.40.1-6) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../105-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../106-libxt6_1%3a1.1.5-1+b3_amd64.deb ... Unpacking libxt6:amd64 (1:1.1.5-1+b3) ... Selecting previously unselected package libxmu6:amd64. Preparing to unpack .../107-libxmu6_2%3a1.1.2-2+b3_amd64.deb ... Unpacking libxmu6:amd64 (2:1.1.2-2+b3) ... Selecting previously unselected package libxaw7:amd64. Preparing to unpack .../108-libxaw7_2%3a1.0.13-1+b2_amd64.deb ... Unpacking libxaw7:amd64 (2:1.0.13-1+b2) ... Selecting previously unselected package graphviz. Preparing to unpack .../109-graphviz_2.40.1-6_amd64.deb ... Unpacking graphviz (2.40.1-6) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../110-hdf5-helpers_1.10.4+repack-10_amd64.deb ... Unpacking hdf5-helpers (1.10.4+repack-10) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../111-libaec0_1.0.2-1_amd64.deb ... Unpacking libaec0:amd64 (1.0.2-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../112-libsz2_1.0.2-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.2-1) ... Selecting previously unselected package libaec-dev:amd64. Preparing to unpack .../113-libaec-dev_1.0.2-1_amd64.deb ... Unpacking libaec-dev:amd64 (1.0.2-1) ... Selecting previously unselected package libboost1.67-dev:amd64. Preparing to unpack .../114-libboost1.67-dev_1.67.0-13_amd64.deb ... Unpacking libboost1.67-dev:amd64 (1.67.0-13) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../115-libboost-dev_1.67.0.1_amd64.deb ... Unpacking libboost-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libcppunit-1.14-0:amd64. Preparing to unpack .../116-libcppunit-1.14-0_1.14.0-3_amd64.deb ... Unpacking libcppunit-1.14-0:amd64 (1.14.0-3) ... Selecting previously unselected package libcppunit-dev. Preparing to unpack .../117-libcppunit-dev_1.14.0-3_amd64.deb ... Unpacking libcppunit-dev (1.14.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../118-libgfortran5_8.3.0-7_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-7) ... Selecting previously unselected package libhdf5-103:amd64. Preparing to unpack .../119-libhdf5-103_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-103:amd64 (1.10.4+repack-10) ... Selecting previously unselected package libhdf5-cpp-103:amd64. Preparing to unpack .../120-libhdf5-cpp-103_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-cpp-103:amd64 (1.10.4+repack-10) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../121-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Selecting previously unselected package libjpeg62-turbo-dev:amd64. Preparing to unpack .../122-libjpeg62-turbo-dev_1%3a1.5.2-2+b1_amd64.deb ... Unpacking libjpeg62-turbo-dev:amd64 (1:1.5.2-2+b1) ... Selecting previously unselected package libjpeg-dev. Preparing to unpack .../123-libjpeg-dev_1%3a1.5.2-2_all.deb ... Unpacking libjpeg-dev (1:1.5.2-2) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../124-libhdf5-dev_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-dev (1.10.4+repack-10) ... Selecting previously unselected package libjsoncpp-dev:amd64. Preparing to unpack .../125-libjsoncpp-dev_1.7.4-3_amd64.deb ... Unpacking libjsoncpp-dev:amd64 (1.7.4-3) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../126-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libboost1.67-dev:amd64 (1.67.0-13) ... Setting up libexpat1:amd64 (2.2.6-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libxdot4 (2.40.1-6) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up libxapian30:amd64 (1.4.11-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up hdf5-helpers (1.10.4+repack-10) ... Setting up libdatrie1:amd64 (0.2.12-2) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up libcppunit-1.14-0:amd64 (1.14.0-3) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1c-1) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up liblab-gamut1 (2.40.1-6) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up libnghttp2-14:amd64 (1.37.0-1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libfakeroot:amd64 (1.23-1) ... Setting up libkrb5support0:amd64 (1.17-2) ... Setting up fakeroot (1.23-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-4) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.24.1-1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.2-2+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libpathplan4 (2.40.1-6) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libfribidi0:amd64 (1.0.5-3.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up d-shlibs (0.84) ... Setting up libk5crypto3:amd64 (1.17-2) ... Setting up libltdl7:amd64 (2.4.6-10) ... Setting up libgfortran5:amd64 (8.3.0-7) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up librhash0:amd64 (1.3.8-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libcdt5 (2.40.1-6) ... Setting up libkrb5-3:amd64 (1.17-2) ... Setting up libcgraph6 (2.40.1-6) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libtiff5:amd64 (4.0.10-4) ... Setting up libcppunit-dev (1.14.0-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libjsoncpp-dev:amd64 (1.7.4-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-10) ... Setting up libarchive13:amd64 (3.3.3-4) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libaec-dev:amd64 (1.0.2-1) ... Setting up libjpeg-dev (1:1.5.2-2) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libllvm6.0:amd64 (1:6.0.1-11) ... Setting up libclang1-6.0 (1:6.0.1-11) ... Setting up libthai0:amd64 (0.1.28-2) ... Setting up doxygen (1.8.13-10) ... Setting up libfreetype6:amd64 (2.9.1-3) ... Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-2) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up libgvpr2 (2.40.1-6) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:amd64 (7.64.0-3) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libhdf5-cpp-103:amd64 (1.10.4+repack-10) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhdf5-dev (1.10.4+repack-10) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up cmake (3.13.4-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up po-debconf (1.0.21) ... Setting up libpango-1.0-0:amd64 (1.42.4-6) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcairo2:amd64 (1.16.0-4) ... Setting up libgd3:amd64 (2.2.5-5.1) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-6) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-6) ... Setting up libgvc6 (2.40.1-6) ... Setting up graphviz (2.40.1-6) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-5-amd64 #1 SMP Debian 4.19.37-3 (2019-05-15) amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.7 g++-7_7.4.0-9 g++-8_8.3.0-7 gcc-7_7.4.0-9 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-7-dev_7.4.0-9 libstdc++-8-dev_8.3.0-7 libstdc++6_8.3.0-7 linux-libc-dev_4.19.37-3 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-common_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 cmake_3.13.4-1 cmake-data_3.13.4-1 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-7_7.4.0-9 cpp-8_8.3.0-7 d-shlibs_0.84 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dirmngr_2.2.13-2 doxygen_1.8.13-10 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.45.1-3 eatmydata_105-7 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.3.0-1 g++-7_7.4.0-9 g++-8_8.3.0-7 gcc_4:8.3.0-1 gcc-7_7.4.0-9 gcc-7-base_7.4.0-9 gcc-8_8.3.0-7 gcc-8-base_8.3.0-7 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.13-2 gnupg-l10n_2.2.13-2 gnupg-utils_2.2.13-2 gpg_2.2.13-2 gpg-agent_2.2.13-2 gpg-wks-client_2.2.13-2 gpg-wks-server_2.2.13-2 gpgconf_2.2.13-2 gpgsm_2.2.13-2 gpgv_2.2.13-2 graphviz_2.40.1-6 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-4 libasan4_7.4.0-9 libasan5_8.3.0-7 libassuan0_2.5.2-1 libatomic1_8.3.0-7 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-dev_2.28-10 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-7 libcdt5_2.40.1-6 libcgraph6_2.40.1-6 libcilkrts5_7.4.0-9 libclang1-6.0_1:6.0.1-11 libcom-err2_1.45.1-3 libcppunit-1.14-0_1.14.0-3 libcppunit-dev_1.14.0-3 libcroco3_0.6.12-3 libcurl4_7.64.0-3 libdatrie1_0.2.12-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libeatmydata1_105-7 libedit2_3.1-20181209-1 libelf1_0.176-1.1 libexpat1_2.2.6-1 libext2fs2_1.45.1-3 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libfribidi0_1.0.5-3.1 libgcc-7-dev_7.4.0-9 libgcc-8-dev_8.3.0-7 libgcc1_1:8.3.0-7 libgcrypt20_1.8.4-5 libgd3_2.2.5-5.1 libgdbm-compat4_1.18.1-4 libgdbm5_1.14.1-6+b1 libgdbm6_1.18.1-4 libgfortran5_8.3.0-7 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-3 libgomp1_8.3.0-7 libgpg-error0_1.35-1 libgraphite2-3_1.3.13-7 libgssapi-krb5-2_1.17-2 libgts-0.7-5_0.7.6+darcs121130-4 libgvc6_2.40.1-6 libgvpr2_2.40.1-6 libharfbuzz0b_2.3.1-1 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1-1 libice6_2:1.0.9-2 libicu63_63.1-6 libidn2-0_2.0.5-1 libisl19_0.20-2 libitm1_8.3.0-7 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-2 libkeyutils1_1.6-6 libkrb5-3_1.17-2 libkrb5support0_1.17-2 libksba8_1.3.5-2 liblab-gamut1_2.40.1-6 libldap-2.4-2_2.4.47+dfsg-3 libldap-common_2.4.47+dfsg-3 libllvm6.0_1:6.0.1-11 liblsan0_8.3.0-7 libltdl7_2.4.6-10 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-7 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.37.0-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.42.4-6 libpangocairo-1.0-0_1.42.4-6 libpangoft2-1.0-0_1.42.4-6 libpathplan4_2.40.1-6 libpcre3_2:8.39-12 libperl5.26_5.26.2-7+b1 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.36-6 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libquadmath0_8.3.0-7 libreadline7_7.0-5 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-2 libss2_1.45.1-3 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-7-dev_7.4.0-9 libstdc++-8-dev_8.3.0-7 libstdc++6_8.3.0-7 libsystemd0_241-5 libsz2_1.0.2-1 libtasn1-6_4.13-3 libthai-data_0.1.28-2 libthai0_0.1.28-2 libtiff5_4.0.10-4 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan0_7.4.0-9 libubsan1_8.3.0-7 libuchardet0_0.0.6-3 libudev1_241-5 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libuv1_1.24.1-1 libwebp6_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxapian30_1.4.11-1 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxdot4_2.40.1-6 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-7+b3 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1+b3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-3 login_1:4.5-1.1 lsb-base_10.2019051400 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 procps_2:3.3.15-2 readline-common_7.0-5 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 x11-common_1:7.7+19 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gatb-core Binary: gatb-core, libgatbcore2, libgatbcore-dev, gatb-core-testdata Architecture: any all Version: 1.4.1+git20181225.44d5a44+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Nadiya Sitdykova , Andreas Tille Homepage: https://github.com/GATB/gatb-core Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/gatb-core Vcs-Git: https://salsa.debian.org/med-team/gatb-core.git Build-Depends: debhelper (>= 12~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz Package-List: gatb-core deb science optional arch=any gatb-core-testdata deb science optional arch=all libgatbcore-dev deb libdevel optional arch=any libgatbcore2 deb libs optional arch=any Checksums-Sha1: f6ec13d6cad10e79e62f7e5cb79051121d8983af 2942532 gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz ecf55200d374aa61903f285ecddc94cf72e89e48 92792 gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.debian.tar.xz Checksums-Sha256: ed5e4663654887f401fd040d5e4590432e50af13583c2acbd95ab1fa63ce8575 2942532 gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz c1a52798dbe0e2dbe3b8ff9ade75bfd546574d2cb0a2ef6ea298f96a7ce22656 92792 gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.debian.tar.xz Files: 4a392da3d22f9dcc12163c7013b95edb 2942532 gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz 4e7b7abb30804f2d9b6eb6746c531ecd 92792 gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlyPXqIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHn/BAAlnB6lYOdBmKnQ/Yb00MZdZwtUocTbNUA gz12A+Q8DZKGzlYOvKAn9JI4nbTwFOBIxv0tez8dRYoiEFI72npmFiW9bbXyVjhU CxEd6FNH9elj1EVDouXxNUpG6KuDurUmoOCgY+KxNuMoSjHvYGK62Q7ZyNn5dthb ur/nRXEhI6Sbn9c1Fs6oe7dcd/LdM7ZYQO3iW9DaxUdObeW5v4fk+r6+Z2GsZCtp kBymrEa2jpqgYqAeV+0befwQlkqbdokaGNGnI1OLDh9rTGPlr9nwfFCe7srfJB24 Wz4Zs+ac8ypA8iyP9e1r0E3AbCX1c/uoZJAF/ApxixGccIaZiw9nj/vp3KUWPq5S 3tlPRchdF0UFLLmSJhDHXvRQ69HD14RBbDeNl7QKnEG75DjxL4eu4pQhGwg3bWJC 7CnP7/f18SEWy5bgXmNKEIAAoBQNlS6vzje7cxE7DT6w5dOP/6jRGRfJs8QjJ7D8 d4sTZLeXJOzVPXsqUwqGm1+tT8ROToM0lBtqBQV6Dbqnr7PXySppwqUkwtqzb/zl 30j7wznmBkjVBm2cXeGI0jfDqZSWb/IU9vGl40ju8aA2TeoMXSlsSkxmB1I3gbos TqHP/rtoKC3Al/mtuuNrnhzIPM6oktJC6APFU/ue3sw48OXwn44De08pZXTlm6hp zacNiJACvfA= =W5fh -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Mar 18 09:02:26 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.dsc dpkg-source: info: extracting gatb-core in /<> dpkg-source: info: unpacking gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz dpkg-source: info: unpacking gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_hdf5.patch dpkg-source: info: applying fix_hdf5_includes.patch dpkg-source: info: applying dynamic_lib.patch dpkg-source: info: applying fix_install_location.patch dpkg-source: info: applying set_soversion.patch dpkg-source: info: applying dynamic_linking_of_tools.patch dpkg-source: info: applying multiarch.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gatb-core_1.4.1+git20181225.44d5a44+dfsg-2 sid amd64 --------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gatb-core_1.4.1+git20181225.44d5a44+dfsg-2 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C 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=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-e31d126c-d274-4817-86bb-79360b7cf74a SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c4203 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+git20181225.44d5a44+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=gatb-core dh_auto_clean -O--sourcedirectory=gatb-core dh_autoreconf_clean -O--sourcedirectory=gatb-core dh_clean -O--sourcedirectory=gatb-core dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building gatb-core using existing ./gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building gatb-core in gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.debian.tar.xz dpkg-source: info: building gatb-core in gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.dsc debian/rules build dh build --sourcedirectory=gatb-core dh_update_autotools_config -O--sourcedirectory=gatb-core dh_autoreconf -O--sourcedirectory=gatb-core dh_auto_configure -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ../gatb-core -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CppUnit: found headers (in /usr/include) but not the static library (/usr/include/../lib/libcppunit.a) -- CppUnit FOUND (/usr/include) -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of __uint128 -- Check size of __uint128 - failed -- Check size of __uint128_t -- Check size of __uint128_t - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") -- HDF5_LIBRARIES="/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_64-linux-gnu/libz.so/usr/lib/x86_64-linux-gnu/libdl.so/usr/lib/x86_64-linux-gnu/libm.so" -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation CMake Warning (dev) at CMakeLists.txt:238 (set): Cannot set "gatb-core-klist": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- ---------- GATB TESTS ---------- -- ---------- GATB TOOLS ---------- DYNAMIC BINARIES for dbgh5 DYNAMIC BINARIES for dbginfo DYNAMIC BINARIES for leon -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") found components: C CMake Warning (dev) at CMakeLists.txt:265 (set): Cannot set "gatb-core-flags": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:266 (set): Cannot set "gatb-core-includes": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:267 (set): Cannot set "gatb-core-libraries": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:268 (set): Cannot set "gatb-core-cmake": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/obj-x86_64-linux-gnu debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gatb-core -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/thirdparty /<>/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/include/None/json Scanning dependencies of target gatbcore-static make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/include/None/BooPHF make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/obj-x86_64-linux-gnu/include/None/BooPHF/ [ 0%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankAlbum.cpp [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core/thirdparty/json/json.hpp /<>/obj-x86_64-linux-gnu/include/None/json/ cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/Bank.cpp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target gatbcore-dynamic make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build [ 1%] Built target thirdparty_copy [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/Bank.cpp /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&value, sizeof(value), 1, file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 3%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankAlbum.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/logging.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/ograph.cpp /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&value, sizeof(value), 1, file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Frontline.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankFasta.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankHelpers.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Terminator.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankRandom.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/Configuration.cpp [ 14%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/logging.cpp [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core/src/gatb/bcalm2/ograph.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Frontline.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/Model.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o -c /<>/gatb-core/src/gatb/system/impl/System.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /<>/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o -c /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret = pthread_attr_init ( &tattr ) ; ^~~ [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o -c /<>/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /<>/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/Leon.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o -c /<>/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /<>/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/api/Data.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/api/Data.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/api/Data.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/gatb_core.hpp:71, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /<>/gatb-core/src/gatb/gatb_core.hpp:40, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o -c /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /<>/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 35%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<32>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<32>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/Configuration.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/Model.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /<>/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o -c /<>/gatb-core/src/gatb/system/impl/System.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /<>/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o -c /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret = pthread_attr_init ( &tattr ) ; ^~~ [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o -c /<>/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /<>/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/Leon.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/gatb_core.hpp:71, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /<>/gatb-core/src/gatb/gatb_core.hpp:40, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o -c /<>/gatb-core/src/gatb/tools/compression/RangeCoder.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o -c /<>/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /<>/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/api/Data.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /<>/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o -c /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /<>/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<32>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<32>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /<>/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of ‘void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here /<>/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable ‘debug_index’ [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of ‘void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]’: /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /<>/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable ‘first_index’ [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp [ 73%] Linking CXX static library ../lib/None/libgatbcore.a cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-static.dir/link.txt --verbose=1 /usr/bin/ar qc ../lib/None/libgatbcore.a CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/api/Data.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ /usr/bin/ranlib ../lib/None/libgatbcore.a make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 73%] Built target gatbcore-static [ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’ /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, short unsigned int> >*, std::allocator, short unsigned int> >*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/test/unit /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/test/unit /<>/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= Scanning dependencies of target gatb-core-cppunit make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 75%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o -c /<>/gatb-core/test/unit/src/bank/TestBank.cpp [ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp [ 76%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o -c /<>/gatb-core/test/unit/src/bank/TestLeon.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core/test/unit/src/bank/TestLeon.cpp:32: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 76%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o -c /<>/gatb-core/test/unit/src/bank/TestSequence.cpp [ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp [ 78%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o -c /<>/gatb-core/test/unit/src/bcalm/TestBcalm.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 78%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o -c /<>/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 78%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o -c /<>/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt8; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt8]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt8’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 79%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o -c /<>/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:33: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 80%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o -c /<>/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:33: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 81%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o -c /<>/gatb-core/test/unit/src/kmer/TestDSK.cpp [ 81%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 81%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o -c /<>/gatb-core/test/unit/src/kmer/TestDebloom.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 81%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o -c /<>/gatb-core/test/unit/src/kmer/TestKmer.cpp [ 81%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp [ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp [ 83%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o -c /<>/gatb-core/test/unit/src/kmer/TestKmerBank.cpp [ 84%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 84%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o -c /<>/gatb-core/test/unit/src/kmer/TestMPHF.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/test/unit/src/kmer/TestMPHF.cpp:27: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o -c /<>/gatb-core/test/unit/src/main.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o -c /<>/gatb-core/test/unit/src/system/TestSystem.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o -c /<>/gatb-core/test/unit/src/tools/collections/TestBag.cpp [ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o -c /<>/gatb-core/test/unit/src/tools/collections/TestCollection.cpp [ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o -c /<>/gatb-core/test/unit/src/tools/collections/TestContainer.cpp [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o -c /<>/gatb-core/test/unit/src/tools/collections/TestIterable.cpp [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o -c /<>/gatb-core/test/unit/src/tools/collections/TestMap.cpp [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o -c /<>/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/test/unit/src/tools/collections/TestMap.cpp:24: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 88%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o -c /<>/gatb-core/test/unit/src/tools/math/TestMath.cpp [ 88%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -c /<>/gatb-core/test/unit/src/tools/misc/TestMisc.cpp [ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -I/<>/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -c /<>/gatb-core/test/unit/src/tools/storage/TestStorage.cpp make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= Scanning dependencies of target dbginfo make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/CMakeFiles/dbginfo.dir/dbginfo.cpp.o cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbginfo.dir/dbginfo.cpp.o -c /<>/gatb-core/tools/dbginfo.cpp In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:23: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::tools::math::NativeInt64; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::tools::math::NativeInt64]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class gatb::core::tools::math::NativeInt64’; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:31: /<>/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/tools/dbginfo.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 90%] Linking CXX executable ../bin/None/dbginfo cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm [ 90%] Linking CXX executable ../../bin/None/gatb-core-cppunit cd /<>/obj-x86_64-linux-gnu/test/unit && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatb-core-cppunit.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -o ../../bin/None/gatb-core-cppunit -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm -lcppunit make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 90%] Built target dbginfo make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= Scanning dependencies of target dbgh5 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbgh5.dir/dbgh5.cpp.o -c /<>/gatb-core/tools/dbgh5.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/tools/dbgh5.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core/tools/dbgh5.cpp: In function ‘void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)’: /<>/gatb-core/tools/dbgh5.cpp:127:13: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] ::system (cmd.str().c_str()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable ../bin/None/dbgh5 cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbgh5.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbgh5.dir/dbgh5.cpp.o -o ../bin/None/dbgh5 -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 91%] Built target gatb-core-cppunit make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= Scanning dependencies of target leon make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/CMakeFiles/leon.dir/leon.cpp.o cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/leon.dir/leon.cpp.o -c /<>/gatb-core/tools/leon.cpp [ 91%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp [ 92%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core/tools/leon.cpp:20: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 92%] Built target dbgh5 [ 92%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp [ 93%] Linking CXX executable ../bin/None/leon cd /<>/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/leon.dir/leon.cpp.o -o ../bin/None/leon -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target leon [ 93%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 94%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp [ 94%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 95%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp [ 95%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 95%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp [ 96%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<128>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<96>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<64>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ In file included from /<>/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp: In instantiation of ‘gatb::core::tools::storage::impl::HDF5IteratorPatch::HDF5IteratorPatch(gatb::core::tools::storage::impl::IterableHDF5Patch*, size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count; size_t = long unsigned int]’: /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:48: required from ‘gatb::core::tools::dp::Iterator* gatb::core::tools::storage::impl::IterableHDF5Patch::iterator() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:436:16: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct gatb::core::kmer::impl::Kmer<>::Count’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] memset (_data, 0, _blockSize*sizeof(Item)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: ‘struct gatb::core::kmer::impl::Kmer<>::Count’ declared here struct Count : tools::misc::Abundance ^~~~~ [ 96%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp [ 97%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 97%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 97%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 98%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 98%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [100%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [100%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/obj-x86_64-linux-gnu/include -I/<>/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core/src -I/<>/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /<>/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [100%] Linking CXX shared library ../lib/None/libgatbcore.so cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-dynamic.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgatbcore.so.2 -o ../lib/None/libgatbcore.so.2 CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/None/libgatbcore.so.2 ../lib/None/libgatbcore.so.2 ../lib/None/libgatbcore.so make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target gatbcore-dynamic make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/<>' echo "Save time of autobuilders and do nothing ... unfortunately this does not seem to work" Save time of autobuilders and do nothing ... unfortunately this does not seem to work make[1]: Leaving directory '/<>' dh_auto_test -O--sourcedirectory=gatb-core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=gatb-core dh_testroot -O--sourcedirectory=gatb-core dh_prep -O--sourcedirectory=gatb-core dh_auto_install -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gatb-core -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/thirdparty /<>/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/include/None/json make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/include/None/BooPHF make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/obj-x86_64-linux-gnu/include/None/BooPHF/ cd /<>/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core/thirdparty/json/json.hpp /<>/obj-x86_64-linux-gnu/include/None/json/ make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build [ 0%] Built target thirdparty_copy make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-dynamic.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-static.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 42%] Built target gatbcore-dynamic [ 86%] Built target gatbcore-static make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/tools /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools /<>/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core /<>/gatb-core/test/unit /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/test/unit /<>/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbgh5.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/leon.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 87%] Built target dbgh5 make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/unit/CMakeFiles/gatb-core-cppunit.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 88%] Built target dbginfo [ 89%] Built target leon [100%] Built target gatb-core-cppunit make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank16.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank12.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank27.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank9.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank22.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank17.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank24.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank11.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank23.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank26.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank25.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank19.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank20.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank15.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank10.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank18.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank14.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank21.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank28.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank13.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/Makefile -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/README.md -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage10.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage9.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/storage/storage7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/protos -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/protos/MicroSNP.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/protos/histo2D.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer16.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer17.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer14.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer12.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer9.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer10.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer13.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer15.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer11.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/observer1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators9.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/optionsparser1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/ToyTool.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/optionsparser2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/iterators4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/tools/multithreading7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn24.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn11.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn15.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn5.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn22.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn18.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn3.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/traversal2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn16.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn27.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn17.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn20.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn21.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn14.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn8.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn2.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/traversal1.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn19.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn23.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn10.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn12.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn26.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn6.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn25.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn4.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn13.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn7.cpp -- Installing: /<>/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn9.cpp -- Installing: /<>/debian/tmp/usr/./README.txt -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.a -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 CMake Error at src/cmake_install.cmake:51 (file): file INSTALL cannot copy file "/<>/obj-x86_64-linux-gnu/lib/None/libgatbcore.so.2" to "/<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so.2". Call Stack (most recent call first): cmake_install.cmake:50 (include) make[1]: *** [Makefile:89: install] Error 1 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_install: cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-06-07T23:26:43Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 3859956 Build-Time: 611 Distribution: sid Fail-Stage: build Host Architecture: amd64 Install-Time: 36 Job: /srv/debomatic/incoming/gatb-core_1.4.1+git20181225.44d5a44+dfsg-2.dsc Machine Architecture: amd64 Package: gatb-core Package-Time: 656 Source-Version: 1.4.1+git20181225.44d5a44+dfsg-2 Space: 3859956 Status: attempted Version: 1.4.1+git20181225.44d5a44+dfsg-2 -------------------------------------------------------------------------------- Finished at 2019-06-07T23:26:43Z Build needed 00:10:56, 3859956k disk space