https://launchpad.net/ubuntu/+source/gatb-core/1.4.1+dfsg-2build1/+build/15767133 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-008 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 12 Dec 10:22:06 ntpdate[1839]: adjust time server 10.211.37.1 offset 0.010565 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15767133 /home/buildd/filecache-default/727e394105280e93a16c79dcca0079cc298d61c4 Creating target for build PACKAGEBUILD-15767133 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15767133 Starting target for build PACKAGEBUILD-15767133 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15767133 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15767133 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15767133 Updating target for build PACKAGEBUILD-15767133 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 Packages [993 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [8917 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5147 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [52.8 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [28.1 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [312 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [156 kB] Fetched 16.6 MB in 8s (2003 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: apt base-files binutils binutils-common binutils-i686-linux-gnu cpp cpp-8 dash dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot findutils g++ g++-8 gcc gcc-8 gcc-8-base grep hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libdb5.3 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi6 libgcc-8-dev libgcc1 libgcrypt20 libgdbm-compat4 libgmp10 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libkmod2 libmpfr6 libmpx2 libnettle6 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libss2 libssl1.1 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 linux-libc-dev lockfile-progs openssl perl perl-base sed systemd systemd-sysv tar tzdata 79 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 56.8 MB of archives. After this operation, 43.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main i386 base-files i386 10.1ubuntu8 [60.2 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main i386 tar i386 1.30+dfsg-3 [264 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dpkg i386 1.19.2ubuntu2 [1124 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 dash i386 0.5.10.2-1 [94.4 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 findutils i386 4.6.0+git+20181018-1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 grep i386 3.1-3 [159 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 hostname i386 3.21 [11.6 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 perl-modules-5.28 all 5.28.1-3 [2812 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm6 i386 1.18.1-2 [32.0 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm-compat4 i386 1.18.1-2 [6700 B] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 libperl5.28 i386 5.28.1-3 [3432 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 perl i386 5.28.1-3 [204 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 perl-base i386 5.28.1-3 [1601 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 libdb5.3 i386 5.3.28+dfsg1-0.2 [737 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 sed i386 4.5-2 [189 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 init-system-helpers all 1.56 [38.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 libquadmath0 i386 8.2.0-12ubuntu1 [208 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 libubsan1 i386 8.2.0-12ubuntu1 [138 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8-base i386 8.2.0-12ubuntu1 [18.6 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 libgcc1 i386 1:8.2.0-12ubuntu1 [48.1 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main i386 libitm1 i386 8.2.0-12ubuntu1 [30.8 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 libasan5 i386 8.2.0-12ubuntu1 [376 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 libgomp1 i386 8.2.0-12ubuntu1 [80.7 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libatomic1 i386 8.2.0-12ubuntu1 [9620 B] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 libmpx2 i386 8.2.0-12ubuntu1 [13.0 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 cpp-8 i386 8.2.0-12ubuntu1 [7539 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 libcc1-0 i386 8.2.0-12ubuntu1 [41.9 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8 i386 8.2.0-12ubuntu1 [8332 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 g++-8 i386 8.2.0-12ubuntu1 [8440 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++-8-dev i386 8.2.0-12ubuntu1 [1587 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 libgcc-8-dev i386 8.2.0-12ubuntu1 [2300 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++6 i386 8.2.0-12ubuntu1 [430 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main i386 libgmp10 i386 2:6.1.2+dfsg-4 [250 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main i386 libmpfr6 i386 4.0.1-2 [246 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 libbinutils i386 2.31.1-10ubuntu1 [521 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main i386 binutils-common i386 2.31.1-10ubuntu1 [194 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 binutils i386 2.31.1-10ubuntu1 [3392 B] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 binutils-i686-linux-gnu i386 2.31.1-10ubuntu1 [1989 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libudev1 i386 239-7ubuntu15 [58.4 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 libapt-pkg5.0 i386 1.8.0~alpha2ubuntu1 [889 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 libnettle6 i386 3.4.1~rc1-1 [128 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 libhogweed4 i386 3.4.1~rc1-1 [142 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 libgnutls30 i386 3.6.4-2ubuntu2 [758 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 libseccomp2 i386 2.3.3-3ubuntu2 [35.6 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 apt i386 1.8.0~alpha2ubuntu1 [1208 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 systemd-sysv i386 239-7ubuntu15 [9400 B] Get:47 http://ftpmaster.internal/ubuntu disco/main i386 libapparmor1 i386 2.12-4ubuntu10 [31.3 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main i386 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:49 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-1build1 [11.1 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 libaudit1 i386 1:2.8.3-1ubuntu3 [40.0 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 libgpg-error0 i386 1.32-3 [60.5 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 libkmod2 i386 25-1ubuntu2 [47.6 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 systemd i386 239-7ubuntu15 [3072 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 libsystemd0 i386 239-7ubuntu15 [229 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 libext2fs2 i386 1.44.4-2ubuntu1 [185 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main i386 e2fsprogs i386 1.44.4-2ubuntu1 [549 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 init i386 1.56 [6652 B] Get:58 http://ftpmaster.internal/ubuntu disco/main i386 libgcrypt20 i386 1.8.4-3ubuntu1 [401 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main i386 libselinux1 i386 2.8-1build2 [73.5 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage-common all 2.8-1build2 [6892 B] Get:61 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage1 i386 2.8-1build2 [93.8 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main i386 libffi6 i386 3.2.1-9 [17.3 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main i386 libcom-err2 i386 1.44.4-2ubuntu1 [9192 B] Get:64 http://ftpmaster.internal/ubuntu disco/main i386 libss2 i386 1.44.4-2ubuntu1 [11.6 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main i386 libdevmapper1.02.1 i386 2:1.02.145-4.1ubuntu4 [125 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main i386 dmsetup i386 2:1.02.145-4.1ubuntu4 [70.4 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main i386 libip4tc0 i386 1.6.1-2ubuntu3 [20.4 kB] Get:68 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libsqlite3-0 i386 3.26.0-3 [566 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main i386 libssl1.1 i386 1.1.1a-1ubuntu2 [1295 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main i386 openssl i386 1.1.1a-1ubuntu2 [627 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018g-1 [188 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main i386 g++ i386 4:8.2.0-2ubuntu2 [1616 B] Get:73 http://ftpmaster.internal/ubuntu disco/main i386 gcc i386 4:8.2.0-2ubuntu2 [5272 B] Get:74 http://ftpmaster.internal/ubuntu disco/main i386 cpp i386 4:8.2.0-2ubuntu2 [27.6 kB] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:76 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main i386 e2fslibs i386 1.44.4-2ubuntu1 [2712 B] Get:78 http://ftpmaster.internal/ubuntu disco/main i386 libfakeroot i386 1.23-1 [26.2 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main i386 fakeroot i386 1.23-1 [63.6 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main i386 libcomerr2 i386 1.44.4-2ubuntu1 [2712 B] Get:81 http://ftpmaster.internal/ubuntu disco-proposed/main i386 linux-libc-dev i386 4.19.0-8.9 [1036 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main i386 lockfile-progs i386 0.1.18 [9856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.8 MB in 3s (17.7 MB/s) (Reading database ... 12644 files and directories currently 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Preparing to unpack .../base-files_10.1ubuntu8_i386.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-3_i386.deb ... Unpacking tar (1.30+dfsg-3) over (1.30+dfsg-2) ... Setting up tar (1.30+dfsg-3) ... (Reading database ... 12643 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_i386.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.0.5ubuntu5) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12629 files and directories currently installed.) 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Setting up libgcc-8-dev:i386 (8.2.0-12ubuntu1) ... Setting up binutils (2.31.1-10ubuntu1) ... Setting up libstdc++-8-dev:i386 (8.2.0-12ubuntu1) ... Setting up libdpkg-perl (1.19.2ubuntu2) ... Setting up gcc-8 (8.2.0-12ubuntu1) ... Setting up g++-8 (8.2.0-12ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15767133 i386 disco-proposed -c chroot:build-PACKAGEBUILD-15767133 --arch=i386 --dist=disco-proposed --nolog gatb-core_1.4.1+dfsg-2build1.dsc Initiating build PACKAGEBUILD-15767133 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-008.buildd +==============================================================================+ | gatb-core 1.4.1+dfsg-2build1 (i386) 12 Dec 2018 10:23 | +==============================================================================+ Package: gatb-core Version: 1.4.1+dfsg-2build1 Source Version: 1.4.1+dfsg-2build1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/gatb-core-WKVMbY/gatb-core-1.4.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gatb-core-WKVMbY' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15767133/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gatb-core_1.4.1+dfsg-2build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-z0Hnmg/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-z0Hnmg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-z0Hnmg/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-z0Hnmg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-z0Hnmg/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-z0Hnmg/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (68.4 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-z0Hnmg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14501 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz Filtered Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz dpkg-deb: building package 'sbuild-build-depends-gatb-core-dummy' in '/<>/resolver-OrDKvo/apt_archive/sbuild-build-depends-gatb-core-dummy.deb'. Ign:1 copy:/<>/resolver-OrDKvo/apt_archive ./ InRelease Get:2 copy:/<>/resolver-OrDKvo/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-OrDKvo/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-OrDKvo/apt_archive ./ Sources [265 B] Get:5 copy:/<>/resolver-OrDKvo/apt_archive ./ Packages [584 B] Fetched 2968 B in 0s (45.0 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install gatb-core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. 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 file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.67-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-7 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhcrypto4-heimdal libhdf5-103 libhdf5-cpp-103 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm7 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsz2 libthai-data libthai0 libtiff5 libtool libuv1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf 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 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl 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 file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.67-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-7 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhcrypto4-heimdal libhdf5-103 libhdf5-cpp-103 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm7 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsz2 libthai-data libthai0 libtiff5 libtool libuv1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf sbuild-build-depends-gatb-core-dummy ucf x11-common zlib1g-dev 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. 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libasn1-8-heimdal i386 7.5.0+dfsg-2.1 [186 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-2.1 [32.2 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-2.1 [93.4 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main i386 libwind0-heimdal i386 7.5.0+dfsg-2.1 [48.4 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-2.1 [117 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-2.1 [230 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-2.1 [16.3 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-2.1 [106 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [15.6 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [52.8 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 libldap-common all 2.4.46+dfsg-5ubuntu3 [16.0 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 libldap-2.4-2 i386 2.4.46+dfsg-5ubuntu3 [166 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main i386 libnghttp2-14 i386 1.35.0-1 [84.2 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2 [58.3 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main i386 libcurl4 i386 7.61.0-1ubuntu2.2 [240 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main i386 libjsoncpp1 i386 1.7.4-3 [82.7 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main i386 librhash0 i386 1.3.6-3 [90.7 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main i386 libuv1 i386 1.24.0-1 [74.8 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main i386 cmake i386 3.12.3-3 [3664 kB] Get:63 http://ftpmaster.internal/ubuntu disco/universe i386 d-shlibs all 0.82+nmu1 [10.2 kB] 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all 11.5.3ubuntu1 [888 kB] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libllvm7 i386 1:7.0.1~+rc3-1 [12.9 MB] Get:76 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libclang1-7 i386 1:7.0.1~+rc3-1 [5866 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main i386 libxapian30 i386 1.4.9-1 [961 kB] Get:78 http://ftpmaster.internal/ubuntu disco/universe i386 doxygen i386 1.8.13-10ubuntu1 [3974 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main i386 libfreetype6 i386 2.8.1-2ubuntu2 [351 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main i386 fonts-dejavu-core all 2.37-1 [1041 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main i386 fontconfig-config all 2.13.0-5ubuntu3 [28.4 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main i386 libfontconfig1 i386 2.13.0-5ubuntu3 [122 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main i386 fontconfig i386 2.13.0-5ubuntu3 [170 kB] Get:84 http://ftpmaster.internal/ubuntu disco/universe i386 libcdt5 i386 2.40.1-5build2 [19.6 kB] Get:85 http://ftpmaster.internal/ubuntu disco/universe i386 libcgraph6 i386 2.40.1-5build2 [44.6 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main i386 libjpeg-turbo8 i386 2.0.0-0ubuntu2 [126 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main i386 libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:88 http://ftpmaster.internal/ubuntu disco/main i386 libjbig0 i386 2.1-3.1build1 [27.3 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main i386 libwebp6 i386 0.6.1-2 [197 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main i386 libtiff5 i386 4.0.10-3 [168 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main i386 libxpm4 i386 1:3.5.12-1 [35.8 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main i386 libgd3 i386 2.2.5-5 [123 kB] Get:93 http://ftpmaster.internal/ubuntu disco/universe i386 libgts-0.7-5 i386 0.7.6+darcs121130-4 [153 kB] Get:94 http://ftpmaster.internal/ubuntu disco/main i386 libpixman-1-0 i386 0.34.0-2 [235 kB] Get:95 http://ftpmaster.internal/ubuntu 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http://ftpmaster.internal/ubuntu disco/main i386 libpangoft2-1.0-0 i386 1.42.4-4 [38.3 kB] Get:107 http://ftpmaster.internal/ubuntu disco/main i386 libpangocairo-1.0-0 i386 1.42.4-4 [24.6 kB] Get:108 http://ftpmaster.internal/ubuntu disco/universe i386 libpathplan4 i386 2.40.1-5build2 [22.5 kB] Get:109 http://ftpmaster.internal/ubuntu disco/universe i386 libgvc6 i386 2.40.1-5build2 [629 kB] Get:110 http://ftpmaster.internal/ubuntu disco/universe i386 libgvpr2 i386 2.40.1-5build2 [181 kB] Get:111 http://ftpmaster.internal/ubuntu disco/universe i386 liblab-gamut1 i386 2.40.1-5build2 [177 kB] Get:112 http://ftpmaster.internal/ubuntu disco/main i386 libxt6 i386 1:1.1.5-1 [164 kB] Get:113 http://ftpmaster.internal/ubuntu disco/main i386 libxmu6 i386 2:1.1.2-2 [48.4 kB] Get:114 http://ftpmaster.internal/ubuntu disco/main i386 libxaw7 i386 2:1.0.13-1 [182 kB] Get:115 http://ftpmaster.internal/ubuntu disco/universe i386 graphviz i386 2.40.1-5build2 [557 kB] Get:116 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 hdf5-helpers i386 1.10.4+repack-1 [12.8 kB] Get:117 http://ftpmaster.internal/ubuntu disco/universe i386 libaec0 i386 1.0.2-1 [21.6 kB] Get:118 http://ftpmaster.internal/ubuntu disco/main i386 libboost1.67-dev i386 1.67.0-11 [8362 kB] Get:119 http://ftpmaster.internal/ubuntu disco/main i386 libboost-dev i386 1.67.0.1 [3232 B] Get:120 http://ftpmaster.internal/ubuntu disco/universe i386 libcppunit-1.14-0 i386 1.14.0-3 [85.2 kB] Get:121 http://ftpmaster.internal/ubuntu disco/universe i386 libcppunit-dev i386 1.14.0-3 [144 kB] Get:122 http://ftpmaster.internal/ubuntu disco/main i386 libgfortran5 i386 8.2.0-12ubuntu1 [556 kB] Get:123 http://ftpmaster.internal/ubuntu disco/universe i386 libsz2 i386 1.0.2-1 [5196 B] Get:124 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libhdf5-103 i386 1.10.4+repack-1 [1278 kB] Get:125 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libhdf5-cpp-103 i386 1.10.4+repack-1 [129 kB] Get:126 http://ftpmaster.internal/ubuntu disco/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] Get:127 http://ftpmaster.internal/ubuntu disco/main i386 libjpeg-turbo8-dev i386 2.0.0-0ubuntu2 [257 kB] Get:128 http://ftpmaster.internal/ubuntu disco/main i386 libjpeg8-dev i386 8c-2ubuntu8 [1546 B] Get:129 http://ftpmaster.internal/ubuntu disco/main i386 libjpeg-dev i386 8c-2ubuntu8 [1544 B] Get:130 http://ftpmaster.internal/ubuntu disco/universe i386 libaec-dev i386 1.0.2-1 [19.8 kB] Get:131 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 libhdf5-dev i386 1.10.4+repack-1 [2711 kB] Get:132 http://ftpmaster.internal/ubuntu disco/main i386 libjsoncpp-dev i386 1.7.4-3 [85.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.1 MB in 3s (22.3 MB/s) Selecting previously unselected package libxau6:i386. 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Setting up libhdf5-cpp-103:i386 (1.10.4+repack-1) ... Setting up libhdf5-dev (1.10.4+repack-1) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libgssapi-krb5-2:i386 (1.16.1-1ubuntu1) ... Setting up libxcb-shm0:i386 (1.13.1-1) ... Setting up libxpm4:i386 (1:3.5.12-1) ... Setting up libxt6:i386 (1:1.1.5-1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up fontconfig (2.13.0-5ubuntu3) ... Regenerating fonts cache... done. Setting up libxext6:i386 (2:1.3.3-1) ... Setting up libgd3:i386 (2.2.5-5) ... Setting up libxmu6:i386 (2:1.1.2-2) ... Setting up libldap-2.4-2:i386 (2.4.46+dfsg-5ubuntu3) ... Setting up libpango-1.0-0:i386 (1.42.4-4) ... Setting up libxaw7:i386 (2:1.0.13-1) ... Setting up libcairo2:i386 (1.16.0-1) ... Setting up libcurl4:i386 (7.61.0-1ubuntu2.2) ... 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Processing triggers for systemd (239-7ubuntu15) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (i686) Toolchain package versions: binutils_2.31.1-10ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-12ubuntu1 gcc-8_8.2.0-12ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-12ubuntu1 libstdc++6_8.2.0-12ubuntu1 linux-libc-dev_4.19.0-8.9 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-10ubuntu1 binutils-common_2.31.1-10ubuntu1 binutils-i686-linux-gnu_2.31.1-10ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 cmake_3.12.3-3 cmake-data_3.12.3-3 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-12ubuntu1 d-shlibs_0.82+nmu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.5.3ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 doxygen_1.8.13-10ubuntu1 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.4-2ubuntu1 e2fsprogs_1.44.4-2ubuntu1 fakeroot_1.23-1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.0-5ubuntu3 fontconfig-config_2.13.0-5ubuntu3 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-12ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-12ubuntu1 gcc-8-base_8.2.0-12ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 graphviz_2.40.1-5build2 grep_3.1-3 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hdf5-helpers_1.10.4+repack-1 hostname_3.21 init_1.56 init-system-helpers_1.56 initscripts_2.88dsf-59.3ubuntu2 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libcurl4_7.61.0-1ubuntu2.2 libdatrie1_0.2.12-1 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libedit2_3.1-20180525-1 libelf1_0.175-1 libexpat1_2.2.6-1 libext2fs2_1.44.4-2ubuntu1 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfontconfig1_2.13.0-5ubuntu3 libfreetype6_2.8.1-2ubuntu2 libfribidi0_1.0.5-3 libgcc-8-dev_8.2.0-12ubuntu1 libgcc1_1:8.2.0-12ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgd3_2.2.5-5 libgdbm-compat4_1.18.1-2 libgdbm5_1.14.1-6 libgdbm6_1.18.1-2 libgfortran5_8.2.0-12ubuntu1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-12ubuntu1 libgpg-error0_1.32-3 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libgts-0.7-5_0.7.6+darcs121130-4 libgvc6_2.40.1-5build2 libgvpr2_2.40.1-5build2 libharfbuzz0b_2.1.1-1build1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libhdf5-103_1.10.4+repack-1 libhdf5-cpp-103_1.10.4+repack-1 libhdf5-dev_1.10.4+repack-1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhx509-5-heimdal_7.5.0+dfsg-2.1 libice6_2:1.0.9-2 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-12ubuntu1 libjbig0_2.1-3.1build1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.0-0ubuntu2 libjpeg-turbo8-dev_2.0.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 liblab-gamut1_2.40.1-5build2 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 libllvm7_1:7.0.1~+rc3-1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 libltdl7_2.4.6-6 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libmpx2_8.2.0-12ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.0-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpango-1.0-0_1.42.4-4 libpangocairo-1.0-0_1.42.4-4 libpangoft2-1.0-0_1.42.4-4 libpathplan4_2.40.1-5build2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.34.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libquadmath0_8.2.0-12ubuntu1 libreadline7_7.0-5 librhash0_1.3.6-3 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.26.0-3 libss2_1.44.4-2ubuntu1 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-12ubuntu1 libstdc++6_8.2.0-12ubuntu1 libsystemd0_239-7ubuntu15 libsz2_1.0.2-1 libtasn1-6_4.13-3 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff5_4.0.10-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libubsan1_8.2.0-12ubuntu1 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libuv1_1.24.0-1 libwebp6_0.6.1-2 libwind0-heimdal_7.5.0+dfsg-2.1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxapian30_1.4.9-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.13.1-1 libxcb-shm0_1.13.1-1 libxcb1_1.13.1-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-7ubuntu3 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.19.0-8.9 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gatb-core-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-3 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 ucf_3.0038 util-linux_2.32-0.1ubuntu2 x11-common_1:7.7+19ubuntu8 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Dec 12 10:21:02 2018 UTC gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+dfsg-2build1.dsc dpkg-source: info: extracting gatb-core in gatb-core-1.4.1+dfsg dpkg-source: info: unpacking gatb-core_1.4.1+dfsg.orig.tar.xz dpkg-source: info: unpacking gatb-core_1.4.1+dfsg-2build1.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 disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15767133 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15767133 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15767133 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+dfsg-2build1 dpkg-buildpackage: info: source distribution disco dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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 debian/rules build-arch dh build-arch --sourcedirectory=gatb-core dh_update_autotools_config -a -O--sourcedirectory=gatb-core dh_autoreconf -a -O--sourcedirectory=gatb-core dh_auto_configure -a -O--sourcedirectory=gatb-core cd obj-i686-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/i386-linux-gnu ../gatb-core -- The C compiler identification is GNU 8.2.0 -- The CXX compiler identification is GNU 8.2.0 -- 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 - failed -- 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/i386-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/i386-linux-gnu/libpthread.so;/usr/lib/i386-linux-gnu/libsz.so;/usr/lib/i386-linux-gnu/libz.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libm.so (found version "1.10.4") -- HDF5_LIBRARIES="/usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/i386-linux-gnu/libpthread.so/usr/lib/i386-linux-gnu/libsz.so/usr/lib/i386-linux-gnu/libz.so/usr/lib/i386-linux-gnu/libdl.so/usr/lib/i386-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/i386-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/i386-linux-gnu/libpthread.so;/usr/lib/i386-linux-gnu/libsz.so;/usr/lib/i386-linux-gnu/libz.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-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: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu dh_auto_build -a -O--sourcedirectory=gatb-core cd obj-i686-linux-gnu && make V=1 -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -H/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-i686-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[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/ cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/json/json.hpp /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/json/ make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 0%] Built target thirdparty_copy Scanning dependencies of target gatbcore-static make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build Scanning dependencies of target gatbcore-dynamic make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 3%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core-1.4.1+dfsg/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 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp: In function ‘long unsigned int gatb::core::debruijn::impl::logging(std::__cxx11::string)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] snprintf (tmp, sizeof(tmp), " memory [current, maxRSS]: [%4lu, %4lu] MB ", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mem, memMaxProcess); ~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp: In function ‘long unsigned int gatb::core::debruijn::impl::logging(std::__cxx11::string)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] snprintf (tmp, sizeof(tmp), " memory [current, maxRSS]: [%4lu, %4lu] MB ", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mem, memMaxProcess); ~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:31:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 19%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp: In member function ‘void gatb::core::kmer::impl::Repartitor::printInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:308:12: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] printf("Repartitor : nbMinimizers=%ld\n", nbMinimizers); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:309:61: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] for (u_int64_t ii=0; ii>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core-1.4.1+dfsg/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 ) ; ^~~ [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::createBloom()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:323:47: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Abundance threshold"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:328:49: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Abundance threshold"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::executeCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:404:43: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: FastQ"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:410:66: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Quality compression: LOSSLESS mode"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:412:106: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Quality compression: lossy mode (use '-lossless' for lossless compression)"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:422:43: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: FastA"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:429:123: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: unknown. Input extension must be one among fasta (.fa, .fasta) or fastq (.fq, .fastq)"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:727:40: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endHeaderCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:883:44: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End Header compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endDnaCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:970:47: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End Sequence compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::executeDecompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1429:38: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "Decompression"); ^ [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp: In member function ‘void gatb::core::kmer::impl::Repartitor::printInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:308:12: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] printf("Repartitor : nbMinimizers=%ld\n", nbMinimizers); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:309:61: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] for (u_int64_t ii=0; ii>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core-1.4.1+dfsg/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 ) ; ^~~ [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp: In member function ‘virtual void gatb::core::tools::misc::impl::ProgressTimerAndSystem::fillBuffer(double)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] snprintf (tmp, sizeof(tmp), " cpu: %5.1f %% mem: [%4lu, %4lu, %4lu] MB ", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:352:9: mem, _memMax, memMaxProcess ~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp: In member function ‘virtual void gatb::core::tools::misc::impl::Properties::setInt(const string&, const int64_t&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] snprintf (buffer, sizeof(buffer), "%ld", value); ^~~~~ ~~~~~ [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/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/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp [ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::createBloom()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:323:47: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Abundance threshold"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:328:49: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Abundance threshold"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::executeCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:404:43: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: FastQ"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:410:66: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Quality compression: LOSSLESS mode"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:412:106: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Quality compression: lossy mode (use '-lossless' for lossless compression)"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:422:43: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: FastA"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:429:123: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add (0, "Input format: unknown. Input extension must be one among fasta (.fa, .fasta) or fastq (.fq, .fastq)"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:727:40: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endHeaderCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:883:44: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End Header compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::endDnaCompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:970:47: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "End Sequence compression"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp: In member function ‘void Leon::executeDecompression()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1429:38: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] getInfo()->add(0, "Decompression"); ^ [ 47%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp: In member function ‘virtual void gatb::core::tools::misc::impl::ProgressTimerAndSystem::fillBuffer(double)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] snprintf (tmp, sizeof(tmp), " cpu: %5.1f %% mem: [%4lu, %4lu, %4lu] MB ", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:352:9: mem, _memMax, memMaxProcess ~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:350:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp: In member function ‘virtual void gatb::core::tools::misc::impl::Properties::setInt(const string&, const int64_t&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:39: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] snprintf (buffer, sizeof(buffer), "%ld", value); ^~~~~ ~~~~~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp [ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:841:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::unordered_map, std::equal_to, std::allocator > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 128; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<128>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 32; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<32>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 64; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<64>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] [ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/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 ‘unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSoliditySum<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "kmers"); ~~~~~~~~~~~^~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityAll<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityCustom<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityOne<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMax<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorSolidityAbstract::getProperties() const [with unsigned int span = 96; Derived = gatb::core::kmer::impl::CountProcessorSolidityMin<96>]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:150:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:153:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:28, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorDump::getProperties() const [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:159:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:172:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "partitions"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of ‘gatb::core::tools::misc::impl::Properties gatb::core::kmer::impl::CountProcessorHistogram::getProperties() const [with unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:131:35: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] result.add (0, "histogram"); ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:947:8: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: ‘class gatb::core::tools::math::NativeInt8’ declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp [ 72%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:7: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 76%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp [ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >; Edge = gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >; Graph = gatb::core::debruijn::impl::GraphTemplate, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > >, gatb::core::debruijn::impl::Edge_t, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, boost::variant, gatb::core::debruijn::impl::GraphData<32>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<64>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<96>, boost::mpl::l_item, gatb::core::debruijn::impl::GraphData<128>, boost::mpl::l_end> > > > > > >]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:852:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > >, std::less, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > >, std::allocator, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> > > > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp: In instantiation of ‘bool gatb::core::debruijn::impl::MonumentTraversalTemplate::validate_consensuses(std::set >&, gatb::core::debruijn::impl::Path_t&) [with Node = gatb::core::debruijn::impl::Node_t >; Edge = gatb::core::debruijn::impl::Edge_t > >; Graph = gatb::core::debruijn::impl::GraphTemplate >, gatb::core::debruijn::impl::Edge_t > >, boost::variant > >]’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:18:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:714:23: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set > >, std::less > > >, std::allocator > > > >::size_type’ {aka ‘unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp [ 82%] Linking CXX shared library ../lib/None/libgatbcore.so cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgatbcore.so.0 -o ../lib/None/libgatbcore.so.0 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 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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 In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 83%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/None/libgatbcore.so.0 ../lib/None/libgatbcore.so.0 ../lib/None/libgatbcore.so make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 83%] Built target gatbcore-dynamic [ 83%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:32, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 83%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 84%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 84%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 85%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:31, from /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:3: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp: In static member function ‘static gatb::core::tools::misc::IProperties& gatb::core::tools::misc::impl::HostInfo::getInfo()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:60:34: warning: ISO C++ forbids converting a string constant to ‘va_list’ {aka ‘char*’} [-Wwrite-strings] props->add (0, "host"); ^ [ 85%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 85%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 86%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 86%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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 /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 87%] Linking CXX static library ../lib/None/libgatbcore.a cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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 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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 /usr/bin/ranlib ../lib/None/libgatbcore.a make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 87%] Built target gatbcore-static make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= Scanning dependencies of target dbgh5 Scanning dependencies of target leon Scanning dependencies of target dbginfo make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 87%] Building CXX object tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp [ 88%] Building CXX object tools/CMakeFiles/dbginfo.dir/dbginfo.cpp.o [ 88%] Building CXX object tools/CMakeFiles/leon.dir/leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/tools/dbginfo.cpp cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/tools/leon.cpp Scanning dependencies of target gatb-core-cppunit make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function ‘void gatb::tests::TestBank::bank_checkSample1_aux(const string&, gatb::core::bank::impl::BankFasta::Iterator::CommentMode_e)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:118:47: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] snprintf (buffer, sizeof(buffer), "seq%ld%s", i+1, (mode == BankFasta::Iterator::FULL ? " generic" : "")); ^~~~~~~~~~ ~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function ‘void gatb::tests::TestBank::bank_checkSample2_aux(const string&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:187:47: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] snprintf (buffer, sizeof(buffer), "seq%ld", nbSeq+1); ^~~~~~~~ ~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp: In member function ‘void gatb::tests::TestBank::bank_perf1()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘u_int64_t’ {aka ‘long long unsigned int’} [-Wformat=] printf ("size=%ld time=%ld => rate=%.3f MB/s \n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalSize, t1-t0, ~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:678:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘gatb::core::system::ITime::Value’ {aka ‘long long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/leon.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbginfo.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp: In function ‘void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)’: /<>/gatb-core-1.4.1+dfsg/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()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 90%] Linking CXX executable ../bin/None/leon cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/leon.dir/leon.cpp.o -o ../bin/None/leon -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm [ 90%] Linking CXX executable ../bin/None/dbginfo cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 90%] Built target leon [ 90%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp [ 90%] Linking CXX executable ../bin/None/dbgh5 cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbgh5.dir/dbgh5.cpp.o -o ../bin/None/dbgh5 -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 90%] Built target dbginfo [ 90%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:32: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 90%] Built target dbgh5 [ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp [ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /<>/gatb-core-1.4.1+dfsg/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 ^~~~~ [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/main.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:27: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp [ 96%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.cpp [ 96%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestContainer.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestIterable.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None/BooPHF/BooPHF.h:545:11: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] printf("rank array : size %lu \n",_ranks.size()); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ [ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp [ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp [100%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -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-1.4.1+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:23: /<>/gatb-core-1.4.1+dfsg/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 = unsigned int]’: /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /<>/gatb-core-1.4.1+dfsg/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-1.4.1+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:31: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: ‘class gatb::core::tools::math::NativeInt64’ declared here class NativeInt64 ^~~~~~~~~~~ [100%] Linking CXX executable ../../bin/None/gatb-core-cppunit cd /<>/gatb-core-1.4.1+dfsg/obj-i686-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=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -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/bcalm/TestBcalm.cpp.o 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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/i386-linux-gnu/hdf5/serial: ../../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/i386-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm -lcppunit make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [100%] Built target gatb-core-cppunit make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' dh_auto_test -a -O--sourcedirectory=gatb-core create-stamp debian/debhelper-build-stamp 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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 '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' cd 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'/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-dynamic.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-static.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' [ 43%] Built target gatbcore-static [ 87%] Built target gatbcore-dynamic 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 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Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankHelpers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankRandom.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankStrings.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankConverterAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankAlbum.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/Bank.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankBinary.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/Alphabet.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankComposite.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/AbstractBank.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankFasta.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankSplitter.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/impl/Banks.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/api/IBank.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/api/IAlphabet.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank/api/Sequence.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/IteratorHelpers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/Observer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/Command.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/IObserver.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/ICommand.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/Iterator.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/OptionsParser.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Pool.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/StringLine.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Property.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/XmlReader.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/TimeInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Stringify.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Algorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Progress.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Histogram.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/HostInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Tokenizer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/LibraryInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Tool.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IOptionsParser.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Enums.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IProperty.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Macros.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/StringsRepository.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Range.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IHistogram.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Data.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Abundance.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Hash16.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionAbstract.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Bloom.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BooPHF.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/ContainerSet.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagPartition.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IterableHelpers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IteratorFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/MapMPHF.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionCache.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/OAHash.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagCache.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BloomGroup.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Bag.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Iterable.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Container.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Collection.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageTools.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageHDF5.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Cell.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5Patch.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.tpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/api/ICell.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/Integer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt2.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt1.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt16.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt32.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt64.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt128.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/FastMinimizer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt8.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/Leon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/HeaderCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/DnaCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/RangeCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/CompressionUtils.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/UnitigsConstructionAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Traversal.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Simplifications.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Terminator.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Graph.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/LinkTigs.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ExtremityInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Frontline.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/dag_vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/NodesDeleter.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/rank_vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ContainerNode.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/IterativeExtensions.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/GraphUnitigs.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/BranchingAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/api/IContainerNode.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/config.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test/gatb-core-cppunit -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test/gatb-core-cppunit" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads3.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample1.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/README.md -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/query.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon1.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/microsnp.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon2.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample1.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/query.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/album.txt -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample.fastq.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/celegans_reads.h5 -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon1.fastq.leon-ref -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample2.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1_list_ids.txt -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads2.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon2.fastq.leon-ref -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbgh5 -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbgh5" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbginfo -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbginfo" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/leon -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/leon" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/BooPHF -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/BooPHF/BooPHF.h make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_install -a d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev gatb-core/cmake usr/lib \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libgatbcore-dev/usr/lib/i386-linux-gnu install -d -m 755 debian/libgatbcore0/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libgatbcore.a debian/libgatbcore-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libgatbcore.so debian/libgatbcore-dev/usr/lib/i386-linux-gnu mv /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libgatbcore.so.0 debian/libgatbcore0/usr/lib/i386-linux-gnu PKGDEV=libgatbcore-dev PKGSHL=libgatbcore0 install -d -m 755 debian/libgatbcore-dev/usr mv debian/tmp/usr/include debian/libgatbcore-dev/usr install -d -m 755 debian/libgatbcore-dev/usr/lib/i386-linux-gnu mv gatb-core/cmake debian/libgatbcore-dev/usr/lib/i386-linux-gnu mkdir -p debian/gatb-core/usr/lib/gatb-core make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' dh_installdocs -a -O--sourcedirectory=gatb-core dh_installchangelogs -a -O--sourcedirectory=gatb-core dh_installexamples -a -O--sourcedirectory=gatb-core dh_installman -a -O--sourcedirectory=gatb-core dh_installcatalogs -a -O--sourcedirectory=gatb-core dh_installcron -a -O--sourcedirectory=gatb-core dh_installdebconf -a -O--sourcedirectory=gatb-core dh_installemacsen -a -O--sourcedirectory=gatb-core dh_installifupdown -a -O--sourcedirectory=gatb-core dh_installinfo -a -O--sourcedirectory=gatb-core dh_installinit -a -O--sourcedirectory=gatb-core dh_installsystemd -a -O--sourcedirectory=gatb-core dh_installmenu -a -O--sourcedirectory=gatb-core dh_installmime -a -O--sourcedirectory=gatb-core dh_installmodules -a -O--sourcedirectory=gatb-core dh_installlogcheck -a -O--sourcedirectory=gatb-core dh_installlogrotate -a -O--sourcedirectory=gatb-core dh_installpam -a -O--sourcedirectory=gatb-core dh_installppp -a -O--sourcedirectory=gatb-core dh_installudev -a -O--sourcedirectory=gatb-core dh_installgsettings -a -O--sourcedirectory=gatb-core dh_bugfiles -a -O--sourcedirectory=gatb-core dh_ucf -a -O--sourcedirectory=gatb-core dh_lintian -a -O--sourcedirectory=gatb-core dh_gconf -a -O--sourcedirectory=gatb-core dh_gconf: Please migrate to dh_installgsettings; gconf + dh_gconf is scheduled for removal. dh_icons -a -O--sourcedirectory=gatb-core dh_perl -a -O--sourcedirectory=gatb-core dh_usrlocal -a -O--sourcedirectory=gatb-core dh_link -a -O--sourcedirectory=gatb-core dh_installwm -a -O--sourcedirectory=gatb-core dh_installxfonts -a -O--sourcedirectory=gatb-core dh_strip_nondeterminism -a -O--sourcedirectory=gatb-core dh_compress -a -O--sourcedirectory=gatb-core dh_fixperms -a -O--sourcedirectory=gatb-core dh_missing -a -O--sourcedirectory=gatb-core dh_strip -a -O--sourcedirectory=gatb-core dh_makeshlibs -a -O--sourcedirectory=gatb-core dh_shlibdeps -a -O--sourcedirectory=gatb-core dpkg-shlibdeps: warning: symbol H5Aexists used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dclose used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dwrite used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Aclose used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Awrite used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateEnd used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzflush used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Tcopy used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5check_version used by debian/libgatbcore0/usr/lib/i386-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: 57 other similar warnings have been skipped (use -v to see them all) dh_installdeb -a -O--sourcedirectory=gatb-core dh_gencontrol -a -O--sourcedirectory=gatb-core dpkg-gencontrol: warning: Depends field of package libgatbcore-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a -O--sourcedirectory=gatb-core dh_builddeb -a -O--sourcedirectory=gatb-core INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libgatbcore-dev (in debian/libgatbcore-dev); do_strip: , oemstrip: pkgstriptranslations: processing libgatbcore0 (in debian/libgatbcore0); do_strip: , oemstrip: pkgstriptranslations: processing gatb-core (in debian/gatb-core); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libgatbcore-dev/DEBIAN/control, package libgatbcore-dev, directory debian/libgatbcore-dev INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... pkgstripfiles: processing control file: debian/gatb-core/DEBIAN/control, package gatb-core, directory debian/gatb-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package gatb-core ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gatb-core' in '../gatb-core_1.4.1+dfsg-2build1_i386.deb'. INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... pkgstripfiles: processing control file: debian/libgatbcore0/DEBIAN/control, package libgatbcore0, directory debian/libgatbcore0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatbcore0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatbcore0' in '../libgatbcore0_1.4.1+dfsg-2build1_i386.deb'. Searching for duplicated docs in dependency libgatbcore0... symlinking changelog.Debian.gz in libgatbcore-dev to file in libgatbcore0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatbcore-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatbcore-dev' in '../libgatbcore-dev_1.4.1+dfsg-2build1_i386.deb'. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing gatb-core-dbgsym (in debian/.debhelper/gatb-core/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/gatb-core/dbgsym-root/DEBIAN/control, package gatb-core-dbgsym, directory debian/.debhelper/gatb-core/dbgsym-root dpkg-deb: building package 'gatb-core-dbgsym' in 'debian/.debhelper/scratch-space/build-gatb-core/gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.deb'. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libgatbcore0-dbgsym (in debian/.debhelper/libgatbcore0/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libgatbcore0/dbgsym-root/DEBIAN/control, package libgatbcore0-dbgsym, directory debian/.debhelper/libgatbcore0/dbgsym-root dpkg-deb: building package 'libgatbcore0-dbgsym' in 'debian/.debhelper/scratch-space/build-libgatbcore0/libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.deb'. Renaming gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.deb to gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.ddeb Renaming libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.deb to libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../gatb-core_1.4.1+dfsg-2build1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181212-1126 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gatb-core_1.4.1+dfsg-2build1_i386.changes: ------------------------------------------ Format: 1.8 Date: Wed, 12 Dec 2018 11:21:00 +0100 Source: gatb-core Binary: gatb-core libgatbcore0 libgatbcore-dev gatb-core-testdata Architecture: i386 Version: 1.4.1+dfsg-2build1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gianfranco Costamagna Description: gatb-core - Genome Analysis Toolbox with de-Bruijn graph gatb-core-testdata - Genome Analysis Toolbox with de-Bruijn graph (test data) libgatbcore-dev - development library of the Genome Analysis Toolbox libgatbcore0 - dynamic library of the Genome Analysis Toolbox Changes: gatb-core (1.4.1+dfsg-2build1) disco; urgency=medium . * Rebuild against new libhdf5-103. Checksums-Sha1: 629342062b93673753c87cfda5d5c53d825afa81 56143128 gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.ddeb f6aea1816f60bedf74bf5ed42abe821283cd3d0d 9718 gatb-core_1.4.1+dfsg-2build1_i386.buildinfo c3b864bdd0144b7bf777ae3f5e6b16ac69550634 1897172 gatb-core_1.4.1+dfsg-2build1_i386.deb 7b927637b9119eded3dfca347f91f7bf0d8d8c46 4076600 libgatbcore-dev_1.4.1+dfsg-2build1_i386.deb 69fbe462f90bc002c9bc49a4b3d971f945ddfe1d 54332252 libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.ddeb 28b476d769837cbcb718ba6ffcfb2cc91156f434 1783308 libgatbcore0_1.4.1+dfsg-2build1_i386.deb Checksums-Sha256: e2ecd039deb7d0ddb40bb877f0eb5f237fd0a9b8bc30143771ec0bef65be58a5 56143128 gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.ddeb 50c346fe7f499b27cb9edf9fa9f21d796de5fedbf37892f825481609642796bb 9718 gatb-core_1.4.1+dfsg-2build1_i386.buildinfo 3a25e8fc0e0b84052344b58ef9f178bf2d7dd45f1933c57158533269ae5928b0 1897172 gatb-core_1.4.1+dfsg-2build1_i386.deb 0bac62bce237d0bf5aed22ee422515da67c7196ff1130761e068bddf30313052 4076600 libgatbcore-dev_1.4.1+dfsg-2build1_i386.deb 5009710623e17c0da8157aac08290da00bcd6e5281ae90ff30fd6cff52f36c1d 54332252 libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.ddeb 7371d183c4a50203729e86083999616ffd10f40d5e501dc4053c2629d95ab33b 1783308 libgatbcore0_1.4.1+dfsg-2build1_i386.deb Files: 2d24850664ed1b4f1e149f644506226f 56143128 debug optional gatb-core-dbgsym_1.4.1+dfsg-2build1_i386.ddeb 684795b5f76ff73d4aff745fb78b4a96 9718 science optional gatb-core_1.4.1+dfsg-2build1_i386.buildinfo dd2ce1b2e61c32db475000108f22bba1 1897172 science optional gatb-core_1.4.1+dfsg-2build1_i386.deb 70121a56cacb2b17e61cbd0834d7c3b6 4076600 libdevel optional libgatbcore-dev_1.4.1+dfsg-2build1_i386.deb 338898d997217013fcbc7699e1d48dde 54332252 debug optional libgatbcore0-dbgsym_1.4.1+dfsg-2build1_i386.ddeb 37dbe976790d7354033ab1f30146e3a1 1783308 libs optional libgatbcore0_1.4.1+dfsg-2build1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gatb-core_1.4.1+dfsg-2build1_i386.deb ------------------------------------- new debian package, version 2.0. size 1897172 bytes: control archive=1220 bytes. 1103 bytes, 22 lines control 553 bytes, 9 lines md5sums Package: gatb-core Version: 1.4.1+dfsg-2build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 14612 Depends: libc6 (>= 2.27), libgcc1 (>= 1:4.2), libhdf5-103, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/GATB/gatb-core Description: Genome Analysis Toolbox with de-Bruijn graph The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/bin/ -rwxr-xr-x root/root 6543092 2018-12-12 10:21 ./usr/bin/dbgh5 -rwxr-xr-x root/root 6530796 2018-12-12 10:21 ./usr/bin/dbginfo -rwxr-xr-x root/root 1832568 2018-12-12 10:21 ./usr/bin/leon drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/lib/gatb-core/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/doc/gatb-core/ -rw-r--r-- root/root 3802 2017-12-14 05:52 ./usr/share/doc/gatb-core/README.txt -rw-r--r-- root/root 311 2018-12-12 10:21 ./usr/share/doc/gatb-core/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-07-06 10:01 ./usr/share/doc/gatb-core/copyright drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/man/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/man/man1/ -rw-r--r-- root/root 1391 2018-12-12 10:21 ./usr/share/man/man1/dbgh5.1.gz -rw-r--r-- root/root 300 2018-12-12 10:21 ./usr/share/man/man1/dbginfo.1.gz -rw-r--r-- root/root 652 2018-12-12 10:21 ./usr/share/man/man1/leon.1.gz libgatbcore-dev_1.4.1+dfsg-2build1_i386.deb ------------------------------------------- new debian package, version 2.0. size 4076600 bytes: control archive=7860 bytes. 1172 bytes, 26 lines control 23947 bytes, 280 lines md5sums Package: libgatbcore-dev Source: gatb-core Version: 1.4.1+dfsg-2build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 59514 Depends: libgatbcore0 (= 1.4.1+dfsg-2build1) Section: libdevel Priority: optional Homepage: https://github.com/GATB/gatb-core Description: development library of the Genome Analysis Toolbox The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ . This package contains the static library and the header files of the gatb-core library. drwxr-xr-x root/root 0 2018-12-12 10:21 ./ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/BooPHF/ -rw-r--r-- root/root 33854 2018-12-12 10:21 ./usr/include/BooPHF/BooPHF.h drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/bank/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/bank/api/ -rw-r--r-- root/root 2480 2017-12-14 05:52 ./usr/include/gatb/bank/api/IAlphabet.hpp -rw-r--r-- root/root 7380 2017-12-14 05:52 ./usr/include/gatb/bank/api/IBank.hpp -rw-r--r-- root/root 10441 2017-12-14 05:52 ./usr/include/gatb/bank/api/Sequence.hpp drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/bank/impl/ -rw-r--r-- root/root 3464 2017-12-14 05:52 ./usr/include/gatb/bank/impl/AbstractBank.hpp -rw-r--r-- root/root 2453 2017-12-14 05:52 ./usr/include/gatb/bank/impl/Alphabet.hpp -rw-r--r-- root/root 6527 2017-12-14 05:52 ./usr/include/gatb/bank/impl/Bank.hpp -rw-r--r-- root/root 4914 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankAlbum.hpp -rw-r--r-- root/root 6611 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankBinary.hpp -rw-r--r-- root/root 6467 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankComposite.hpp -rw-r--r-- root/root 3833 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankConverterAlgorithm.hpp -rw-r--r-- root/root 8647 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankFasta.hpp -rw-r--r-- root/root 7447 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankHelpers.hpp -rw-r--r-- root/root 3917 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankRandom.hpp -rw-r--r-- root/root 5133 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankSplitter.hpp -rw-r--r-- root/root 4749 2017-12-14 05:52 ./usr/include/gatb/bank/impl/BankStrings.hpp -rw-r--r-- root/root 1434 2017-12-14 05:52 ./usr/include/gatb/bank/impl/Banks.hpp drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/bcalm2/ -rw-r--r-- root/root 4030 2017-12-14 05:52 ./usr/include/gatb/bcalm2/ThreadPool.h -rw-r--r-- root/root 1436 2017-12-14 05:52 ./usr/include/gatb/bcalm2/bcalm_algo.hpp -rw-r--r-- root/root 4690 2017-12-14 05:52 ./usr/include/gatb/bcalm2/bglue_algo.hpp -rw-r--r-- root/root 1152 2017-12-14 05:52 ./usr/include/gatb/bcalm2/binSeq.h -rw-r--r-- root/root 175 2017-12-14 05:52 ./usr/include/gatb/bcalm2/logging.hpp -rw-r--r-- root/root 3031 2017-12-14 05:52 ./usr/include/gatb/bcalm2/ograph.h -rw-r--r-- root/root 1198 2017-12-14 05:52 ./usr/include/gatb/bcalm2/ographBin.h -rw-r--r-- root/root 18205 2017-12-14 05:52 ./usr/include/gatb/bcalm2/unionFind.hpp drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/debruijn/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/include/gatb/debruijn/api/ -rw-r--r-- root/root 2432 2017-12-14 05:52 ./usr/include/gatb/debruijn/api/IContainerNode.hpp 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./usr/share/doc/libgatbcore-dev/examples/tools/optionsparser1.cpp -rw-r--r-- root/root 749 2017-12-14 05:52 ./usr/share/doc/libgatbcore-dev/examples/tools/optionsparser2.cpp libgatbcore0_1.4.1+dfsg-2build1_i386.deb ---------------------------------------- new debian package, version 2.0. size 1783308 bytes: control archive=1160 bytes. 1133 bytes, 25 lines control 226 bytes, 3 lines md5sums 27 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libgatbcore0 Source: gatb-core Version: 1.4.1+dfsg-2build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9655 Depends: libc6 (>= 2.27), libgcc1 (>= 1:4.2), libstdc++6 (>= 7) Section: libs Priority: optional Homepage: https://github.com/GATB/gatb-core Description: dynamic library of the Genome Analysis Toolbox The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ . This package contains the dynamic library. drwxr-xr-x root/root 0 2018-12-12 10:21 ./ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/lib/i386-linux-gnu/ -rw-r--r-- root/root 9840272 2018-12-12 10:21 ./usr/lib/i386-linux-gnu/libgatbcore.so.0 drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-12 10:21 ./usr/share/doc/libgatbcore0/ -rw-r--r-- root/root 311 2018-12-12 10:21 ./usr/share/doc/libgatbcore0/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-07-06 10:01 ./usr/share/doc/libgatbcore0/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 2555816 Build-Time: 3712 Distribution: disco-proposed Host Architecture: i386 Install-Time: 74 Job: gatb-core_1.4.1+dfsg-2build1.dsc Machine Architecture: amd64 Package: gatb-core Package-Time: 3788 Source-Version: 1.4.1+dfsg-2build1 Space: 2555816 Status: successful Version: 1.4.1+dfsg-2build1 -------------------------------------------------------------------------------- Finished at 20181212-1126 Build needed 01:03:08, 2555816k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15767133 Scanning for processes to kill in build PACKAGEBUILD-15767133