https://launchpad.net/ubuntu/+source/gatb-core/1.4.1+dfsg-3/+build/15783567 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-013 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... 15 Dec 17:09:17 ntpdate[1848]: adjust time server 10.211.37.1 offset 0.000015 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15783567 /home/buildd/filecache-default/020b0022f770b890c357907d03d82568c584d50e Creating target for build PACKAGEBUILD-15783567 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15783567 Starting target for build PACKAGEBUILD-15783567 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15783567 '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-15783567 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15783567 Updating target for build PACKAGEBUILD-15783567 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 amd64 Packages [1006 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8973 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5152 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [74.9 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [36.5 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [761 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [328 kB] Fetched 17.3 MB in 5s (3644 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu dpkg dpkg-dev libassuan0 libbinutils libdpkg-perl libgpg-error0 libsqlite3-0 linux-libc-dev 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6051 kB of archives. After this operation, 80.9 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg amd64 1.19.2ubuntu2 [1101 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgpg-error0 amd64 1.33-3 [57.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-3 [530 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-11ubuntu1 [1829 kB] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libbinutils amd64 2.31.1-11ubuntu1 [484 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils amd64 2.31.1-11ubuntu1 [3396 B] Get:7 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-common amd64 2.31.1-11ubuntu1 [194 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libassuan0 amd64 2.5.2-1 [35.1 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.19.0-9.10 [1041 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6051 kB in 0s (18.2 MB/s) (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_amd64.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.33-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.33-3) over (1.32-3) ... Setting up libgpg-error0:amd64 (1.33-3) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../0-libsqlite3-0_3.26.0-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.26.0-3) over (3.26.0-2) ... Preparing to unpack .../1-binutils-x86-64-linux-gnu_2.31.1-11ubuntu1_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../2-libbinutils_2.31.1-11ubuntu1_amd64.deb ... Unpacking libbinutils:amd64 (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../3-binutils_2.31.1-11ubuntu1_amd64.deb ... Unpacking binutils (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../4-binutils-common_2.31.1-11ubuntu1_amd64.deb ... Unpacking binutils-common:amd64 (2.31.1-11ubuntu1) over (2.31.1-10ubuntu1) ... Preparing to unpack .../5-dpkg-dev_1.19.2ubuntu2_all.deb ... Unpacking dpkg-dev (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Preparing to unpack .../6-libdpkg-perl_1.19.2ubuntu2_all.deb ... Unpacking libdpkg-perl (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Preparing to unpack .../7-libassuan0_2.5.2-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.2-1) over (2.5.1-2) ... Preparing to unpack .../8-linux-libc-dev_4.19.0-9.10_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.19.0-9.10) over (4.18.0-11.12) ... Setting up linux-libc-dev:amd64 (4.19.0-9.10) ... Setting up libdpkg-perl (1.19.2ubuntu2) ... Setting up binutils-common:amd64 (2.31.1-11ubuntu1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:amd64 (3.26.0-3) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libbinutils:amd64 (2.31.1-11ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.31.1-11ubuntu1) ... Setting up binutils (2.31.1-11ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15783567 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15783567 --arch=amd64 --dist=disco-proposed --nolog -A gatb-core_1.4.1+dfsg-3.dsc Initiating build PACKAGEBUILD-15783567 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 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-013.buildd +==============================================================================+ | gatb-core 1.4.1+dfsg-3 (amd64) 15 Dec 2018 17:09 | +==============================================================================+ Package: gatb-core Version: 1.4.1+dfsg-3 Source Version: 1.4.1+dfsg-3 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/gatb-core-WDCRrF/gatb-core-1.4.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gatb-core-WDCRrF' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15783567/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gatb-core_1.4.1+dfsg-3.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-7RIBZx/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-7RIBZx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7RIBZx/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-7RIBZx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7RIBZx/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-7RIBZx/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (249 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 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-7RIBZx/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 ... 12668 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.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-8BxXfW/apt_archive/sbuild-build-depends-gatb-core-dummy.deb'. Ign:1 copy:/<>/resolver-8BxXfW/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8BxXfW/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8BxXfW/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8BxXfW/apt_archive ./ Sources [265 B] Get:5 copy:/<>/resolver-8BxXfW/apt_archive ./ Packages [586 B] Fetched 2970 B in 0s (183 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 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 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 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, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 68.8 MB of archives. After this operation, 382 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8BxXfW/apt_archive ./ sbuild-build-depends-gatb-core-dummy 0.invalid.0 [912 B] Get:2 http://ftpmaster.internal/ubuntu disco/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 libbsd0 amd64 0.9.1-1 [44.6 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 libxdmcp6 amd64 1:1.1.2-3 [10.7 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 libxcb1 amd64 1.13.1-2 [45.2 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 libx11-data all 2:1.6.7-1 [113 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 libx11-6 amd64 2:1.6.7-1 [572 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 groff-base amd64 1.22.3-10 [1153 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main amd64 libpipeline1 amd64 1.5.0-2 [25.7 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main amd64 man-db amd64 2.8.4-3 [1028 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main amd64 x11-common all 1:7.7+19ubuntu8 [22.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main amd64 libice6 amd64 2:1.0.9-2 [40.2 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic-mgc amd64 1:5.34-2 [197 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic1 amd64 1:5.34-2 [72.3 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main amd64 file amd64 1:5.34-2 [22.8 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main amd64 libelf1 amd64 0.175-1 [44.2 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main amd64 libexpat1 amd64 2.2.6-1 [87.2 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main amd64 libfribidi0 amd64 1.0.5-3 [26.1 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main amd64 libglib2.0-0 amd64 2.58.1-2 [1176 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main amd64 libicu63 amd64 63.1-5 [8284 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main amd64 libxml2 amd64 2.9.4+dfsg1-7ubuntu3 [625 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main amd64 ucf all 3.0038 [50.5 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main amd64 gettext-base amd64 0.19.8.1-9 [50.1 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libedit2 amd64 3.1-20181209-1 [85.9 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5support0 amd64 1.16.1-1ubuntu1 [31.0 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libk5crypto3 amd64 1.16.1-1ubuntu1 [85.5 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 libkeyutils1 amd64 1.5.9-9.3 [9640 B] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5-3 amd64 1.16.1-1ubuntu1 [281 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main amd64 libgssapi-krb5-2 amd64 1.16.1-1ubuntu1 [122 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libpsl5 amd64 0.20.2-2 [50.0 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 m4 amd64 1.4.18-2 [199 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 autoconf all 2.69-11 [322 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 automake all 1:1.16.1-4 [522 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 autopoint all 0.19.8.1-9 [412 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 cmake-data all 3.13.2-1 [1457 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libarchive13 amd64 3.3.3-1 [304 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-2.1 [41.4 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-2.1 [182 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-2.1 [29.4 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-2.1 [86.7 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-2.1 [47.8 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-2.1 [107 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-2.1 [206 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-2.1 [14.8 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-2.1 [96.4 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu3 [16.0 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu3 [154 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 libnghttp2-14 amd64 1.35.0-1 [78.9 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 libcurl4 amd64 7.61.0-1ubuntu2.2 [217 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 librhash0 amd64 1.3.6-3 [78.6 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main amd64 libuv1 amd64 1.24.0-1 [69.3 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main amd64 cmake amd64 3.13.2-1 [3466 kB] Get:62 http://ftpmaster.internal/ubuntu disco/universe amd64 d-shlibs all 0.82+nmu1 [10.2 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main amd64 libtool all 2.4.6-6 [195 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main amd64 dh-autoreconf all 19 [16.1 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main amd64 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [13.9 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main amd64 dh-strip-nondeterminism all 1.0.0-1 [5064 B] Get:68 http://ftpmaster.internal/ubuntu disco/main amd64 dwz amd64 0.12-3 [78.1 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main amd64 gettext amd64 0.19.8.1-9 [896 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main amd64 po-debconf all 1.0.21 [233 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main amd64 debhelper all 11.5.3ubuntu1 [888 kB] Get:74 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libllvm7 amd64 1:7.0.1~+rc3-2 [12.9 MB] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libclang1-7 amd64 1:7.0.1~+rc3-2 [5968 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main amd64 libxapian30 amd64 1.4.9-1 [672 kB] Get:77 http://ftpmaster.internal/ubuntu disco/universe amd64 doxygen amd64 1.8.13-10ubuntu1 [3944 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main amd64 libfreetype6 amd64 2.8.1-2ubuntu2 [335 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main amd64 fontconfig-config all 2.13.0-5ubuntu3 [28.4 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main amd64 libfontconfig1 amd64 2.13.0-5ubuntu3 [112 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main amd64 fontconfig amd64 2.13.0-5ubuntu3 [170 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libgraphite2-3 amd64 1.3.12-1 [73.6 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main amd64 libharfbuzz0b amd64 2.1.1-1build1 [328 kB] Get:105 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libpangoft2-1.0-0 amd64 1.42.4-5 [35.3 kB] Get:106 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libpangocairo-1.0-0 amd64 1.42.4-5 [23.1 kB] Get:107 http://ftpmaster.internal/ubuntu disco/universe amd64 libpathplan4 amd64 2.40.1-5build2 [21.9 kB] Get:108 http://ftpmaster.internal/ubuntu disco/universe amd64 libgvc6 amd64 2.40.1-5build2 [600 kB] Get:109 http://ftpmaster.internal/ubuntu disco/universe amd64 libgvpr2 amd64 2.40.1-5build2 [169 kB] Get:110 http://ftpmaster.internal/ubuntu disco/universe amd64 liblab-gamut1 amd64 2.40.1-5build2 [178 kB] Get:111 http://ftpmaster.internal/ubuntu disco/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:112 http://ftpmaster.internal/ubuntu disco/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB] Get:113 http://ftpmaster.internal/ubuntu disco/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:114 http://ftpmaster.internal/ubuntu disco/universe amd64 graphviz amd64 2.40.1-5build2 [559 kB] Get:115 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 hdf5-helpers amd64 1.10.4+repack-1 [12.8 kB] Get:116 http://ftpmaster.internal/ubuntu disco/universe amd64 libaec0 amd64 1.0.2-1 [19.1 kB] Get:117 http://ftpmaster.internal/ubuntu disco/main amd64 libboost1.67-dev amd64 1.67.0-11 [8362 kB] Get:118 http://ftpmaster.internal/ubuntu disco/main amd64 libboost-dev amd64 1.67.0.1 [3228 B] Get:119 http://ftpmaster.internal/ubuntu disco/universe amd64 libcppunit-1.14-0 amd64 1.14.0-3 [77.3 kB] Get:120 http://ftpmaster.internal/ubuntu disco/universe amd64 libcppunit-dev amd64 1.14.0-3 [132 kB] Get:121 http://ftpmaster.internal/ubuntu disco/main amd64 libgfortran5 amd64 8.2.0-12ubuntu1 [587 kB] Get:122 http://ftpmaster.internal/ubuntu disco/universe amd64 libsz2 amd64 1.0.2-1 [5152 B] Get:123 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libhdf5-103 amd64 1.10.4+repack-1 [1292 kB] Get:124 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libhdf5-cpp-103 amd64 1.10.4+repack-1 [121 kB] Get:125 http://ftpmaster.internal/ubuntu disco/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:126 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg-turbo8-dev amd64 2.0.0-0ubuntu2 [238 kB] Get:127 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:128 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:129 http://ftpmaster.internal/ubuntu disco/universe amd64 libaec-dev amd64 1.0.2-1 [16.9 kB] Get:130 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libhdf5-dev amd64 1.10.4+repack-1 [2570 kB] Get:131 http://ftpmaster.internal/ubuntu disco/main amd64 libjsoncpp-dev amd64 1.7.4-3 [85.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.8 MB in 5s (14.4 MB/s) Selecting previously unselected package libxau6:amd64. 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Setting up libltdl7:amd64 (2.4.6-6) ... Setting up libfribidi0:amd64 (1.0.5-3) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libthai-data (0.1.28-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up x11-common (1:7.7+19ubuntu8) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libgfortran5:amd64 (8.2.0-12ubuntu1) ... Setting up hdf5-helpers (1.10.4+repack-1) ... Setting up libcdt5 (2.40.1-5build2) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-9) ... 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Setting up doxygen (1.8.13-10ubuntu1) ... Setting up libaec-dev:amd64 (1.0.2-1) ... Setting up libharfbuzz0b:amd64 (2.1.1-1build1) ... Setting up libtiff5:amd64 (4.0.10-3) ... Setting up autoconf (2.69-11) ... Setting up libthai0:amd64 (0.1.28-1) ... Setting up libhdf5-103:amd64 (1.10.4+repack-1) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up libfontconfig1:amd64 (2.13.0-5ubuntu3) ... Setting up libsm6:amd64 (2:1.2.2-1) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up po-debconf (1.0.21) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libhdf5-cpp-103:amd64 (1.10.4+repack-1) ... Setting up libhdf5-dev (1.10.4+repack-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up fontconfig (2.13.0-5ubuntu3) ... Regenerating fonts cache... done. Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libgd3:amd64 (2.2.5-5) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up libpango-1.0-0:amd64 (1.42.4-5) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libcairo2:amd64 (1.16.0-1) ... Setting up libcurl4:amd64 (7.61.0-1ubuntu2.2) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-5) ... Setting up cmake (3.13.2-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-5) ... Setting up libgvc6 (2.40.1-5build2) ... Setting up graphviz (2.40.1-5build2) ... Setting up dh-strip-nondeterminism (1.0.0-1) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-gatb-core-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Processing triggers for systemd (239-7ubuntu15) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11ubuntu1 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_4.19.0-9.10 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_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 binutils-x86-64-linux-gnu_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 cmake_3.13.2-1 cmake-data_3.13.2-1 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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_3.1-20181209-1 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 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_1.33-3 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~+rc3-2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-12ubuntu1 libltdl7_2.4.6-6 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 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_1.42.4-5 libpangocairo-1.0-0_1.42.4-5 libpangoft2-1.0-0_1.42.4-5 libpathplan4_2.40.1-5build2 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.36.0-1 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 libtsan0_8.2.0-12ubuntu1 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_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 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_4.19.0-9.10 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-5.28_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 Sat Dec 15 10:47:10 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+dfsg-3.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-3.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-15783567 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15783567 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15783567 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-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=gatb-core dh_auto_clean -O--sourcedirectory=gatb-core dh_autoreconf_clean -O--sourcedirectory=gatb-core dh_clean -O--sourcedirectory=gatb-core debian/rules build dh build --sourcedirectory=gatb-core dh_update_autotools_config -O--sourcedirectory=gatb-core dh_autoreconf -O--sourcedirectory=gatb-core dh_auto_configure -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ../gatb-core -- The C compiler identification is GNU 8.2.0 -- 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 - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") -- HDF5_LIBRARIES="/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_64-linux-gnu/libz.so/usr/lib/x86_64-linux-gnu/libdl.so/usr/lib/x86_64-linux-gnu/libm.so" -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation CMake Warning (dev) at CMakeLists.txt:238 (set): Cannot set "gatb-core-klist": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- ---------- GATB TESTS ---------- -- ---------- GATB TOOLS ---------- DYNAMIC BINARIES for dbgh5 DYNAMIC BINARIES for dbginfo DYNAMIC BINARIES for leon -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") found components: C CMake Warning (dev) at CMakeLists.txt:265 (set): Cannot set "gatb-core-flags": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:266 (set): Cannot set "gatb-core-includes": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:267 (set): Cannot set "gatb-core-libraries": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:268 (set): Cannot set "gatb-core-cmake": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_auto_build -a cd obj-x86_64-linux-gnu && make V=1 -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/ cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/json/ make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target gatbcore-static [ 0%] Built target thirdparty_copy make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target gatbcore-dynamic make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build [ 0%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 0%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 /<>/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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 3%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 /<>/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/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 /<>/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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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 = long 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 = long 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 = long 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 = long 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 ^~~~~ [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core-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; ^~ [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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/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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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 = long 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 = long 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 = long 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 = long 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/kmer/impl/MPHFAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 /<>/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-static.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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 = long 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ In file included from /<>/gatb-core-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 = long 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 ^~~~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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 = long 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 = long 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 = long 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 ^~~~~~~~~~~ [ 31%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 31%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 32%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 32%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 32%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 37%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 41%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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 = long 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 ^~~~~~~~~~ [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 44%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 44%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.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 ) ; ^~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-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 long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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/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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t’ {aka ‘long unsigned int’} [-Wformat=] snprintf(temp,200,"%llu",value); ^~~~~~ ~~~~~ [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.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/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 = long 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/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 = long 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 ^~~~~~~~~~ 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-x86_64-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 long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-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 long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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/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 = long 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 = long 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 = long 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-x86_64-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 long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp [ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-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 = long 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-x86_64-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 ^~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-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 long 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 long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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/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 = long 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-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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-x86_64-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 long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 long 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 long unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/obj-x86_64-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 long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/Model.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ 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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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; ^~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/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-x86_64-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 = long 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-x86_64-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 ^~~~~ 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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp [ 61%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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; ^~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ In file included from /<>/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-x86_64-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 = long 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-x86_64-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 ^~~~~ 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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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; ^~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-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 long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:11: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.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/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-x86_64-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 = long 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-x86_64-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 ^~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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]; ^~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp /<>/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 long 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 long unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/obj-x86_64-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 long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 long 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 long unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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/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-x86_64-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 long 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 long 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 ‘long 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 ‘long 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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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]; ^~~~~~~~~ [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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]; ^~~~~~~~~ [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp [ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~ [ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-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 = long 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-x86_64-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 ^~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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]; ^~~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp [ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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]; ^~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 80%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 80%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 81%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 82%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 83%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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-x86_64-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 = long 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-x86_64-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 ^~~~~ [ 84%] Linking CXX static library ../lib/None/libgatbcore.a cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-static.dir/link.txt 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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 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CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o /usr/bin/ranlib ../lib/None/libgatbcore.a make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target gatbcore-static [ 84%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= Scanning dependencies of target gatb-core-cppunit make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= Scanning dependencies of target dbginfo make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 86%] Building CXX object tools/CMakeFiles/dbginfo.dir/dbginfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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/tools/dbginfo.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 87%] Linking CXX executable ../bin/None/dbginfo cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/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/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target dbginfo make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= Scanning dependencies of target dbgh5 make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] /<>/gatb-core-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()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX executable ../bin/None/dbgh5 cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbgh5.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/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/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= Scanning dependencies of target leon make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[4]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 87%] Building CXX object tools/CMakeFiles/leon.dir/leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target dbgh5 [ 88%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-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/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/leon.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 89%] Linking CXX executable ../bin/None/leon cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/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/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 89%] Built target leon [ 90%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 90%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 91%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 91%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 91%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] In file included from /<>/gatb-core-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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 = long 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 ^~~~~ [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 94%] Linking CXX shared library ../lib/None/libgatbcore.so cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-dynamic.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/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 CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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[4]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target gatbcore-dynamic [ 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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:11: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("bit array of size %lli: \n",_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:13: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf(" (%llu) ",ii); ^~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^~~~~~~~~~~~~~~~~ ~~ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] [ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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 = long 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-x86_64-linux-gnu/test/unit && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatb-core-cppunit.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/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 CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o 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'/<>/gatb-core-1.4.1+dfsg' echo "Save time of autobuilders and do nothing ... unfortunately this does not seem to work" Save time of autobuilders and do nothing ... unfortunately this does not seem to work make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' dh_auto_test -O--sourcedirectory=gatb-core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=gatb-core dh_testroot -O--sourcedirectory=gatb-core dh_prep -O--sourcedirectory=gatb-core dh_installdirs -O--sourcedirectory=gatb-core dh_auto_install -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && make V=1 -j4 install DESTDIR=/<>/gatb-core-1.4.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu 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/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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-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-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build [ 88%] Built target dbginfo make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbgh5.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/leon.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/unit/CMakeFiles/gatb-core-cppunit.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target dbgh5 [ 89%] Built target leon [100%] Built target gatb-core-cppunit make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/debruijn -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn18.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn9.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/debruijn/debruijn11.cpp -- Installing: 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/<>/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/Leon.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/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/Collection.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/impl -- 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/OAHash.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/MapMPHF.hpp -- 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/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/ContainerSet.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/CollectionAbstract.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/BooPHF.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/impl/BagCache.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/api -- 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/IHistogram.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/misc/api/IOptionsParser.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/Range.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/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/impl -- 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/Property.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/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/OptionsParser.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/Progress.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/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/XmlReader.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/impl/Histogram.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/NativeInt128.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/FastMinimizer.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/Integer.hpp -- 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/NativeInt8.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/LargeInt.hpp -- 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/api -- 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/designpattern/api/ICommand.hpp -- 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/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/gatb_core.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/template -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bank -- 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/Sequence.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/IBank.hpp -- 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/Banks.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/BankBinary.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/BankAlbum.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/Bank.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/Alphabet.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/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/system -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/IFileSystem.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/ISmartPointer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/ITime.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/IThread.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/Exception.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/IMemory.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/types.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/ISystemInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/config_sha1.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemMacos.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadMacos.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadLinux.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/SystemInfoCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemLinux.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/TimeCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/System.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/MemoryCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2 -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/bcalm_algo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/bglue_algo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/ographBin.h -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/binSeq.h -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/unionFind.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/logging.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/ThreadPool.h -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/bcalm2/ograph.h -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/api/IModel.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/api/ICountProcessor.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessor.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/ConfigurationAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartiInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartitionsCommand.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithmFactory.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/LinearCounter.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Configuration.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorCutoff.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmerIterator.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorProxy.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorHistogram.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorAbstract.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/SortingCountAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BloomBuilder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Sequence2SuperKmer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorSolidity.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomMinimizerAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/RepartitionAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorChain.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorDump.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BloomAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/kmer/impl/MPHFAlgorithm.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/celegans_reads.h5 -- 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/query.fa -- 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/sample1.fa.gz -- 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/leon1.fastq.leon-ref -- 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/reads2.fa -- 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_list_ids.txt -- 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/album.txt -- 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/leon1.fastq -- 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/test//db/reads3.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/sample.fastq.gz -- 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/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-x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libgatbcore0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.a debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mv /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 debian/libgatbcore0/usr/lib/x86_64-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/x86_64-linux-gnu mv gatb-core/cmake debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mkdir -p debian/gatb-core/usr/lib/gatb-core make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_install -i mkdir -p debian/gatb-core/usr/lib/gatb-core mv debian/gatb-core-testdata/usr/share/doc/gatb-core/test/gatb-core-cppunit debian/gatb-core/usr/lib/gatb-core make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' dh_installdocs -O--sourcedirectory=gatb-core dh_installchangelogs -O--sourcedirectory=gatb-core dh_installexamples -O--sourcedirectory=gatb-core dh_installman -O--sourcedirectory=gatb-core dh_installcatalogs -O--sourcedirectory=gatb-core dh_installcron -O--sourcedirectory=gatb-core dh_installdebconf -O--sourcedirectory=gatb-core dh_installemacsen -O--sourcedirectory=gatb-core dh_installifupdown -O--sourcedirectory=gatb-core dh_installinfo -O--sourcedirectory=gatb-core dh_installinit -O--sourcedirectory=gatb-core dh_installsystemd -O--sourcedirectory=gatb-core dh_installmenu -O--sourcedirectory=gatb-core dh_installmime -O--sourcedirectory=gatb-core dh_installmodules -O--sourcedirectory=gatb-core dh_installlogcheck -O--sourcedirectory=gatb-core dh_installlogrotate -O--sourcedirectory=gatb-core dh_installpam -O--sourcedirectory=gatb-core dh_installppp -O--sourcedirectory=gatb-core dh_installudev -O--sourcedirectory=gatb-core dh_installgsettings -O--sourcedirectory=gatb-core dh_bugfiles -O--sourcedirectory=gatb-core dh_ucf -O--sourcedirectory=gatb-core dh_lintian -O--sourcedirectory=gatb-core dh_gconf -O--sourcedirectory=gatb-core dh_gconf: Please migrate to dh_installgsettings; gconf + dh_gconf is scheduled for removal. dh_icons -O--sourcedirectory=gatb-core dh_perl -O--sourcedirectory=gatb-core dh_usrlocal -O--sourcedirectory=gatb-core dh_link -O--sourcedirectory=gatb-core dh_installwm -O--sourcedirectory=gatb-core dh_installxfonts -O--sourcedirectory=gatb-core dh_strip_nondeterminism -O--sourcedirectory=gatb-core dh_compress -O--sourcedirectory=gatb-core dh_fixperms -O--sourcedirectory=gatb-core dh_missing -O--sourcedirectory=gatb-core dh_strip -O--sourcedirectory=gatb-core dh_makeshlibs -O--sourcedirectory=gatb-core dh_shlibdeps -O--sourcedirectory=gatb-core dpkg-shlibdeps: warning: symbol gzwrite used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit_ used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dget_space used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Acreate2 used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateEnd used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dvlen_reclaim used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Pset_shuffle used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5open used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Screate_simple used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit_ used by debian/libgatbcore0/usr/lib/x86_64-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 -O--sourcedirectory=gatb-core dh_gencontrol -O--sourcedirectory=gatb-core dpkg-gencontrol: warning: Depends field of package gatb-core-testdata: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libgatbcore-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--sourcedirectory=gatb-core dh_builddeb -O--sourcedirectory=gatb-core INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing gatb-core (in debian/gatb-core); do_strip: , oemstrip: pkgstriptranslations: processing libgatbcore0 (in debian/libgatbcore0); do_strip: , oemstrip: pkgstriptranslations: processing libgatbcore-dev (in debian/libgatbcore-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gatb-core/DEBIAN/control, package gatb-core, directory debian/gatb-core pkgstripfiles: processing control file: debian/libgatbcore0/DEBIAN/control, package libgatbcore0, directory debian/libgatbcore0 INFO: pkgstripfiles: waiting for lock (libgatbcore0) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package gatb-core ... pkgstripfiles: processing control file: debian/libgatbcore-dev/DEBIAN/control, package libgatbcore-dev, directory debian/libgatbcore-dev pkgstripfiles: No PNG files. dpkg-deb: building package 'gatb-core' in '../gatb-core_1.4.1+dfsg-3_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatbcore0 ... pkgstripfiles: No PNG files. INFO: pkgstripfiles: waiting for lock (libgatbcore-dev) ... dpkg-deb: building package 'libgatbcore0' in '../libgatbcore0_1.4.1+dfsg-3_amd64.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-3_amd64.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-3_amd64.deb'. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing gatb-core-testdata (in debian/gatb-core-testdata); do_strip: , oemstrip: 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 " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gatb-core-testdata/DEBIAN/control, package gatb-core-testdata, directory debian/gatb-core-testdata Searching for duplicated docs in dependency gatb-core... symlinking changelog.Debian.gz in gatb-core-testdata to file in gatb-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package gatb-core-testdata ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gatb-core-testdata' in '../gatb-core-testdata_1.4.1+dfsg-3_all.deb'. 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-3_amd64.deb'. Renaming libgatbcore0-dbgsym_1.4.1+dfsg-3_amd64.deb to libgatbcore0-dbgsym_1.4.1+dfsg-3_amd64.ddeb Renaming gatb-core-dbgsym_1.4.1+dfsg-3_amd64.deb to gatb-core-dbgsym_1.4.1+dfsg-3_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../gatb-core_1.4.1+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181215-1728 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gatb-core_1.4.1+dfsg-3_amd64.changes: ------------------------------------- Format: 1.8 Date: Sat, 15 Dec 2018 10:22:40 +0100 Source: gatb-core Binary: gatb-core libgatbcore0 libgatbcore-dev gatb-core-testdata Architecture: amd64 all Version: 1.4.1+dfsg-3 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille 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 Closes: 903613 Changes: gatb-core (1.4.1+dfsg-3) unstable; urgency=medium . * Make sure target dir exists also for Architecture: all build Closes: #903613 * Standards-Version: 4.2.1 * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/control Checksums-Sha1: 2a84d1eb974ea1670d7150594322acec0bc0c7f7 102408244 gatb-core-dbgsym_1.4.1+dfsg-3_amd64.ddeb 0eb0763231b924609ec045efd83c0181f02acacd 1793828 gatb-core-testdata_1.4.1+dfsg-3_all.deb 7437633ffb696bd13a0b4748b1f87e0c0a38407c 9972 gatb-core_1.4.1+dfsg-3_amd64.buildinfo f8ed683c68c8d0a0bd66bdcb4280e4e78499956c 3443084 gatb-core_1.4.1+dfsg-3_amd64.deb 1c413a3f0232b1bfaf96342692e0b0e30735bf93 3763284 libgatbcore-dev_1.4.1+dfsg-3_amd64.deb c9336845fd072f4ed8417437e04993bd9068a624 57044924 libgatbcore0-dbgsym_1.4.1+dfsg-3_amd64.ddeb 805ba4932ee068e05e456a38ca6c1fbd8272f461 1635932 libgatbcore0_1.4.1+dfsg-3_amd64.deb Checksums-Sha256: 2016b12b4ecc7d4ee353f759c00d8db58e7ddbc9aeb05f9edd50afab32592e91 102408244 gatb-core-dbgsym_1.4.1+dfsg-3_amd64.ddeb ec21e905ec6f9a9119ca760e545cb17162caa556c15e51cfc373281fb1105e66 1793828 gatb-core-testdata_1.4.1+dfsg-3_all.deb 2e4af95748f42e69e594dd1077e896071cded19d5047f940b12d4624f93698f2 9972 gatb-core_1.4.1+dfsg-3_amd64.buildinfo 7ec078c95562690094f3eb9cfa55f4a61b0741ba4e0aad338877ca5a596242f5 3443084 gatb-core_1.4.1+dfsg-3_amd64.deb 659f306ff6ac8877420e4db121dfdba79ade12786f9cee673021f0bab8c364fc 3763284 libgatbcore-dev_1.4.1+dfsg-3_amd64.deb 584516b4ba3a7e62025f9ab7602ddb6c5901476ec0aca2a43db30b2e7d9efd6e 57044924 libgatbcore0-dbgsym_1.4.1+dfsg-3_amd64.ddeb b61991a2e516b1c7bf1e62346176e1c54afca6e7f4c7e08523a8431b0c83165b 1635932 libgatbcore0_1.4.1+dfsg-3_amd64.deb Files: 46d186f3b70de9727872a158a15e10c4 102408244 debug optional gatb-core-dbgsym_1.4.1+dfsg-3_amd64.ddeb 78292a6d84ac6af893e26704e3ca5e06 1793828 science optional gatb-core-testdata_1.4.1+dfsg-3_all.deb 1ccd18feec60845d4e00bb0f5eb68f7c 9972 science optional gatb-core_1.4.1+dfsg-3_amd64.buildinfo 727ab12624c499a21b5cd37d7149c4c7 3443084 science optional gatb-core_1.4.1+dfsg-3_amd64.deb cda6e27daed15b5ec6e76b53d5aa7212 3763284 libdevel optional libgatbcore-dev_1.4.1+dfsg-3_amd64.deb 2d840e0ba403fee38c8f98e738d4a68c 57044924 debug optional libgatbcore0-dbgsym_1.4.1+dfsg-3_amd64.ddeb c77f01ec408d38cf19061a3d709f4a6f 1635932 libs optional libgatbcore0_1.4.1+dfsg-3_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gatb-core-testdata_1.4.1+dfsg-3_all.deb --------------------------------------- new debian package, version 2.0. size 1793828 bytes: control archive=1436 bytes. 1110 bytes, 25 lines control 1526 bytes, 19 lines md5sums Package: gatb-core-testdata Source: gatb-core Version: 1.4.1+dfsg-3 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1818 Depends: gatb-core Section: science Priority: optional Homepage: https://github.com/GATB/gatb-core Description: Genome Analysis Toolbox with de-Bruijn graph (test data) 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 some data to test the library. drwxr-xr-x root/root 0 2018-12-15 09:22 ./ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core-testdata/ lrwxrwxrwx root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core-testdata/changelog.Debian.gz -> ../gatb-core/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-12-15 09:22 ./usr/share/doc/gatb-core-testdata/copyright drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/db/ -rw-r--r-- root/root 762 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/README.md -rw-r--r-- root/root 19 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/album.txt -rw-r--r-- root/root 26648 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/celegans_reads.h5.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon1.fastq -rw-r--r-- root/root 2158 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon1.fastq.leon-ref.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon2.fastq -rw-r--r-- root/root 2158 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon2.fastq.leon-ref.gz -rw-r--r-- root/root 52 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/microsnp.fa -rw-r--r-- root/root 25848 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/query.fa.gz -rw-r--r-- root/root 28676 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads1.fa.gz -rw-r--r-- root/root 4 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads1_list_ids.txt -rw-r--r-- root/root 141726 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads2.fa.gz -rw-r--r-- root/root 1565367 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/db/reads3.fa.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample.fastq -rw-r--r-- root/root 477 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/db/sample.fastq.gz -rw-r--r-- root/root 710 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample1.fa -rw-r--r-- root/root 180 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/db/sample1.fa.gz -rw-r--r-- root/root 131 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample2.fa lrwxrwxrwx root/root 0 2018-12-15 09:22 ./usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit gatb-core_1.4.1+dfsg-3_amd64.deb -------------------------------- new debian package, version 2.0. size 3443084 bytes: control archive=1256 bytes. 1115 bytes, 22 lines control 623 bytes, 10 lines md5sums Package: gatb-core Version: 1.4.1+dfsg-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 24177 Depends: libc6 (>= 2.27), libcppunit-1.14-0, libgcc1 (>= 1:3.0), libhdf5-103, libstdc++6 (>= 7), 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. 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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/ . 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./usr/share/doc/libgatbcore-dev/examples/tools/observer1.cpp -rw-r--r-- root/root 1503 2017-12-14 05:52 ./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-3_amd64.deb ----------------------------------- new debian package, version 2.0. size 1635932 bytes: control archive=1160 bytes. 1128 bytes, 25 lines control 228 bytes, 3 lines md5sums 27 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libgatbcore0 Source: gatb-core Version: 1.4.1+dfsg-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9668 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.0), 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 2018-12-15 09:22 ./ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 9853312 2018-12-15 09:22 ./usr/lib/x86_64-linux-gnu/libgatbcore.so.0 drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-15 09:22 ./usr/share/doc/libgatbcore0/ -rw-r--r-- root/root 353 2018-12-15 09:22 ./usr/share/doc/libgatbcore0/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-12-15 09:22 ./usr/share/doc/libgatbcore0/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 3824380 Build-Time: 1078 Distribution: disco-proposed Host Architecture: amd64 Install-Time: 43 Job: gatb-core_1.4.1+dfsg-3.dsc Machine Architecture: amd64 Package: gatb-core Package-Time: 1122 Source-Version: 1.4.1+dfsg-3 Space: 3824380 Status: successful Version: 1.4.1+dfsg-3 -------------------------------------------------------------------------------- Finished at 20181215-1728 Build needed 00:18:42, 3824380k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15783567 Scanning for processes to kill in build PACKAGEBUILD-15783567