I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 3 18:08:39 +14 2023 I: pbuilder-time-stamp: 1696306119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gatb-core_1.4.1+git20181225.44d5a44+dfsg-3.dsc] I: copying [./gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz] I: copying [./gatb-core_1.4.1+git20181225.44d5a44+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Jun 20 00:58:34 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+git20181225.44d5a44+dfsg-3.dsc dpkg-source: info: extracting gatb-core in gatb-core-1.4.1+git20181225.44d5a44+dfsg dpkg-source: info: unpacking gatb-core_1.4.1+git20181225.44d5a44+dfsg.orig.tar.xz dpkg-source: info: unpacking gatb-core_1.4.1+git20181225.44d5a44+dfsg-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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' lrwxrwxrwx 1 root root 4 Oct 3 18:08 /bin/sh -> bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=61b4aed3304d40d6b883f174b4448902 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1990648 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.one4jv1ChI/pbuilderrc_MSWz --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.one4jv1ChI/b2 --logfile b2/build.log gatb-core_1.4.1+git20181225.44d5a44+dfsg-3.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.18.0-0.deb11.3-amd64 #1 SMP PREEMPT_DYNAMIC Debian 5.18.14-1~bpo11+1 (2022-07-28) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Oct 3 18:08 sh -> bash lrwxrwxrwx 1 root root 4 Sep 10 04:47 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libcppunit-dev; however: Package libcppunit-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang1-6.0{a} libcppunit-1.14-0{a} libcppunit-dev{a} libcroco3{a} libcurl4{a} libdatrie1{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhdf5-103{a} libhdf5-cpp-103{a} libhdf5-dev{a} libice6{a} libicu63{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap-2.4-2{a} libldap-common{a} libllvm6.0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libprocps7{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libsz2{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} ucf{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-liberation krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 79.9 MB of archives. After unpacking 395 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u3 [689 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u1 [1551 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1+deb10u1 [110 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 d-shlibs all 0.84 [17.2 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libllvm6.0 amd64 1:6.0.1-10 [14.7 MB] Get: 63 http://deb.debian.org/debian buster/main amd64 libclang1-6.0 amd64 1:6.0.1-10 [6951 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 doxygen amd64 1.8.13-10 [3985 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libcdt5 amd64 2.40.1-6+deb10u1 [60.7 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libcgraph6 amd64 2.40.1-6+deb10u1 [84.2 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u3 [271 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libgd3 amd64 2.2.5-5.2 [136 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u1 [63.7 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libpathplan4 amd64 2.40.1-6+deb10u1 [63.6 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libxdot4 amd64 2.40.1-6+deb10u1 [57.0 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libgvc6 amd64 2.40.1-6+deb10u1 [646 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libgvpr2 amd64 2.40.1-6+deb10u1 [213 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 liblab-gamut1 amd64 2.40.1-6+deb10u1 [220 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 graphviz amd64 2.40.1-6+deb10u1 [596 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 hdf5-helpers amd64 1.10.4+repack-10 [35.2 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get: 116 http://deb.debian.org/debian buster/main amd64 libaec-dev amd64 1.0.2-1 [18.4 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 119 http://deb.debian.org/debian buster/main amd64 libcppunit-1.14-0 amd64 1.14.0-3 [140 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libcppunit-dev amd64 1.14.0-3 [196 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libhdf5-cpp-103 amd64 1.10.4+repack-10 [146 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo-dev amd64 1:1.5.2-2+deb10u1 [208 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libjpeg-dev all 1:1.5.2-2+deb10u1 [57.7 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libhdf5-dev amd64 1.10.4+repack-10 [2598 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libjsoncpp-dev amd64 1.7.4-3 [86.2 kB] Fetched 79.9 MB in 1s (70.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../006-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../007-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../008-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../009-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../010-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../011-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../012-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../013-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../014-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../015-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../016-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../021-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package cmake-data. Preparing to unpack .../022-cmake-data_3.13.4-1_all.deb ... Unpacking cmake-data (3.13.4-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../023-libicu63_63.1-6+deb10u3_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../024-libxml2_2.9.4+dfsg1-7+deb10u3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../025-libarchive13_3.3.3-4+deb10u1_amd64.deb ... Unpacking libarchive13:amd64 (3.3.3-4+deb10u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../026-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../027-libkrb5support0_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../028-libk5crypto3_1.17-3+deb10u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../029-libssl1.1_1.1.1n-0+deb10u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../030-libkrb5-3_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../031-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../032-libsasl2-modules-db_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../033-libsasl2-2_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Selecting previously unselected package libldap-common. Preparing to unpack .../034-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../035-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../036-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../037-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../038-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../039-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../040-libcurl4_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl4:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../041-libexpat1_2.2.6-2+deb10u4_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u4) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../042-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../043-librhash0_1.3.8-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.8-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../044-libuv1_1.24.1-1+deb10u1_amd64.deb ... Unpacking libuv1:amd64 (1.24.1-1+deb10u1) ... Selecting previously unselected package cmake. Preparing to unpack .../045-cmake_3.13.4-1_amd64.deb ... Unpacking cmake (3.13.4-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../046-d-shlibs_0.84_all.deb ... Unpacking d-shlibs (0.84) ... Selecting previously unselected package libtool. Preparing to unpack .../047-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../048-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../049-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../050-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../051-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../052-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../053-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../054-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../055-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../056-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../057-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../058-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../059-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../060-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm6.0:amd64. 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Setting up po-debconf (1.0.21) ... Setting up libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up libgd3:amd64 (2.2.5-5.2) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libgvc6 (2.40.1-6+deb10u1) ... Setting up graphviz (2.40.1-6+deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_source.changes dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+git20181225.44d5a44+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CppUnit: found headers (in /usr/include) but not the static library (/usr/include/../lib/libcppunit.a) -- CppUnit FOUND (/usr/include) -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of __uint128 -- Check size of __uint128 - failed -- Check size of __uint128_t -- Check size of __uint128_t - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") -- HDF5_LIBRARIES="/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_64-linux-gnu/libz.so/usr/lib/x86_64-linux-gnu/libdl.so/usr/lib/x86_64-linux-gnu/libm.so" -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation CMake Warning (dev) at CMakeLists.txt:238 (set): Cannot set "gatb-core-klist": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- ---------- GATB TESTS ---------- -- ---------- GATB TOOLS ---------- DYNAMIC BINARIES for dbgh5 DYNAMIC BINARIES for dbginfo DYNAMIC BINARIES for leon -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.4") found components: C CMake Warning (dev) at CMakeLists.txt:265 (set): Cannot set "gatb-core-flags": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:266 (set): Cannot set "gatb-core-includes": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:267 (set): Cannot set "gatb-core-libraries": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:268 (set): Cannot set "gatb-core-cmake": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core -B/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/json cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty/json/json.hpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/json/ make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [ 0%] Built target thirdparty_copy Scanning dependencies of target gatbcore-dynamic make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build Scanning dependencies of target gatbcore-static make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp [ 2%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o [ 4%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function 'bool gatb::core::bank::impl::checkMagic(FILE*)': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function 'virtual void gatb::core::bank::impl::BankBinary::Iterator::next()': /build/gatb-core-1.4.1+git20181225.44d5a44+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 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function 'bool gatb::core::bank::impl::checkMagic(FILE*)': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function 'virtual void gatb::core::bank::impl::BankBinary::Iterator::next()': /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 8%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/bank/impl/BankHelpers.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/kmer/impl/BloomBuilder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/kmer/impl/Configuration.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 13%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp [ 16%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 18%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)': /build/gatb-core-1.4.1+git20181225.44d5a44+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 ) ; ^~~ [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/tools/compression/Leon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 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-DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/api/Data.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/tools/misc/impl/TimeInfo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/tools/misc/impl/Tokenizer.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeNumeric()': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeDelta()': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeDelta2()': /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp [ 34%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp [ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 36%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp [ 41%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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); ~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 45%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)': /build/gatb-core-1.4.1+git20181225.44d5a44+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 ) ; ^~~ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeNumeric()': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeDelta()': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function 'void HeaderDecoder::decodeDelta2()': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~ ~~~~~ [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:71, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:48, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ [ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp [ 52%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/api/Data.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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/api/Data.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/api/Data.cpp [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:22: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp:44:7: note: 'class gatb::core::tools::math::NativeInt8' declared here class NativeInt8 : private misc::ArrayData ^~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp [ 61%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp [ 62%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp [ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 65%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp [ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp [ 66%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization7.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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); ~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<64>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ [ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In instantiation of 'void gatb::core::debruijn::impl::graph3::debruijn() [with long unsigned int span = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:31:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:236:10: warning: unused variable 'debug_index' [-Wunused-variable] uint debug_index = 0; ^~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:765:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp: In instantiation of 'void gatb::core::debruijn::impl::determine_order_sequences(std::vector >&, const std::vector >&, int, bool) [with int SPAN = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:1106:48: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:29:9: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:258:18: warning: unused variable 'first_index' [-Wunused-variable] uint32_t first_index = markedSequence_index; ^~~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.h:15, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:5, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 128]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 69%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp [ 70%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 32]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp [ 73%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 96]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) ~~^~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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++) /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:48:7: note: 'class gatb::core::tools::math::NativeInt64' declared here class NativeInt64 ^~~~~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp: In instantiation of 'void gatb::core::kmer::impl::CountProcessorHistogram::end() [with long unsigned int span = 64]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:104:10: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=0; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:120:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int jj=0; jj<= _histogram->getLength2(); jj++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:122:26: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj)); ^~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:135:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for(int ii=1; ii<= _histogram->getLength(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:137:25: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii)); ^~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1057:5: required from 'void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:1048:8: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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) ~~~~~^~~~~~~~~~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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; ~~~~~^~~~~~~~~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:42, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 76%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:45, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~~~~~~ [ 76%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp [ 76%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp [ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:311:21: warning: unused variable 'abundance' [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization5.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp [ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp [ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization6.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization6.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization7.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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/TemplateSpecialization7.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 ^~~~~ [ 82%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ [ 83%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 84%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:37, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+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%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 84%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 85%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 85%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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%] Linking CXX shared library ../lib/None/libgatbcore.so cd /build/gatb-core-1.4.1+git20181225.44d5a44+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 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgatbcore.so.2 -o ../lib/None/libgatbcore.so.2 CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o 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CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/None/libgatbcore.so.2 ../lib/None/libgatbcore.so.2 ../lib/None/libgatbcore.so make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target gatbcore-dynamic [ 86%] Linking CXX static library ../lib/None/libgatbcore.a cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-static.dir/link.txt --verbose=1 /usr/bin/ar qc ../lib/None/libgatbcore.a CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o 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test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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/TestSequence.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbginfo.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:33: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:32: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:27: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:33: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/leon.cpp:20: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/main.cpp [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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=] /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/dbgh5.cpp: In function 'void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)': /build/gatb-core-1.4.1+git20181225.44d5a44+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()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:43, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:25: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1568:12: note: 'struct gatb::core::kmer::impl::Kmer<>::Count' declared here struct Count : tools::misc::Abundance ^~~~~ [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 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cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/leon.dir/leon.cpp.o -o ../bin/None/leon -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm [ 95%] Linking CXX executable ../bin/None/dbgh5 cd /build/gatb-core-1.4.1+git20181225.44d5a44+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 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbgh5.dir/dbgh5.cpp.o -o ../bin/None/dbgh5 -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm [ 96%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 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-I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp [ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o cd 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test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty -I/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src -g -O2 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:24: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const': /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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); ^~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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]); ^~~~~~~~~~~~~~~~~ ~~ /build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [100%] Built target dbgh5 make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [100%] Built target dbginfo In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:34, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666, from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:23: /build/gatb-core-1.4.1+git20181225.44d5a44+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]': /build/gatb-core-1.4.1+git20181225.44d5a44+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]' /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:335:25: required from here /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:31: /build/gatb-core-1.4.1+git20181225.44d5a44+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 /build/gatb-core-1.4.1+git20181225.44d5a44+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 -ffile-prefix-map=/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestSequence.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o 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'/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+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_auto_install -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core -B/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/json make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to 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target dbginfo [ 89%] Built target leon [100%] Built target gatb-core-cppunit make[2]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/share/doc/gatb-core/examples -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/tools -- Installing: 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/template -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/TimeCommon.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadMacos.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadLinux.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/SystemInfoCommon.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/System.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/MemoryCommon.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemMacos.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemLinux.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemCommon.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/types.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/config_sha1.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ITime.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IThread.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ISystemInfo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/ISmartPointer.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IMemory.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/IFileSystem.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/Exception.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/SortingCountAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Sequence2SuperKmer.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/RepartitionAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartitionsCommand.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/PartiInfo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.pri -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Model.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/MPHFAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/LinearCounter.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomMinimizerAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithmFactory.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.pri -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/DebloomAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorSolidity.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorProxy.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorHistogram.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorDump.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorCutoff.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorChain.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessorAbstract.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/CountProcessor.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/ConfigurationAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/Configuration.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BloomBuilder.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BloomAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmers.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/impl/BankKmerIterator.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api/IModel.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/kmer/api/ICountProcessor.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/gatb_core.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/rank_vector.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/dag_vector.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/UnitigsConstructionAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Traversal.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Terminator.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Simplifications.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/NodesDeleter.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/LinkTigs.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/IterativeExtensions.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/GraphUnitigs.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Graph.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Frontline.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ExtremityInfo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ContainerNode.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/BranchingAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/api -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/debruijn/api/IContainerNode.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2 -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/unionFind.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ographBin.h -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ograph.h -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/logging.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/binSeq.h -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/bglue_algo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/bcalm_algo.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bcalm2/ThreadPool.h -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Banks.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankStrings.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankSplitter.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankRandom.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankHelpers.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankFasta.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankConverterAlgorithm.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankComposite.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankBinary.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/BankAlbum.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Bank.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/Alphabet.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/impl/AbstractBank.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/Sequence.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/IBank.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/bank/api/IAlphabet.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/gatb/system/api/config.hpp -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test/gatb-core-cppunit -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test/gatb-core-cppunit" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample2.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample1.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/sample.fastq -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads3.fa.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads2.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1_list_ids.txt -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/reads1.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa.gz -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/query.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/microsnp.fa -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon2.fastq.leon-ref -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon2.fastq -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq.leon-ref -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/leon1.fastq -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/celegans_reads.h5 -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/album.txt -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/test//db/README.md -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbgh5 -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbgh5" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbginfo -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/dbginfo" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/leon -- Set runtime path of "/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/bin/leon" to "" -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/BooPHF -- Installing: /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/include/BooPHF/BooPHF.h make[1]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg' 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/libgatbcore2/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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 debian/libgatbcore2/usr/lib/x86_64-linux-gnu PKGDEV=libgatbcore-dev PKGSHL=libgatbcore2 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 dh_install -a make[1]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+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 '/build/gatb-core-1.4.1+git20181225.44d5a44+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_installinit -O--sourcedirectory=gatb-core dh_installsystemduser -O--sourcedirectory=gatb-core dh_perl -O--sourcedirectory=gatb-core dh_link -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_dwz -O--sourcedirectory=gatb-core dh_strip -O--sourcedirectory=gatb-core dh_makeshlibs -O--sourcedirectory=gatb-core dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below dpkg-gensymbols: warning: debian/libgatbcore2/DEBIAN/symbols doesn't match completely debian/libgatbcore2.symbols.amd64 --- debian/libgatbcore2.symbols.amd64 (libgatbcore2_1.4.1+git20181225.44d5a44+dfsg-3_amd64) +++ dpkg-gensymbolsXgkfJV 2023-10-03 18:16:15.616373434 +1400 @@ -8997,6 +8997,7 @@ _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1 _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1 + _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg-3 _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1 _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1 _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi3EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1 @@ -9006,6 +9007,7 @@ _ZNSt6vectorISt5tupleIJmiEESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 1.4.1 _ZNSt6vectorISt5tupleIJmiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1 _ZNSt6vectorISt6threadSaIS0_EE17_M_realloc_insertIJZN10ThreadPoolC4EmEUlvE_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base 1.4.1 + _ZNSt6vectorIbSaIbEE13_M_initializeEm@Base 1.4.1+git20181225.44d5a44+dfsg-3 _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb@Base 1.4.1 _ZNSt6vectorIbSaIbEE13_M_reallocateEm@Base 1.4.1 _ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb@Base 1.4.1 dh_shlibdeps -O--sourcedirectory=gatb-core dpkg-shlibdeps: warning: symbol H5Dwrite used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Pclose used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Tclose used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateEnd used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Gopen2 used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dset_extent used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol gzwrite used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Aexists used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries dpkg-shlibdeps: warning: 57 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/leon debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/dbginfo debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit were not linked against libsz.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gatb-core/usr/bin/leon debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/dbginfo debian/gatb-core/usr/lib/gatb-core/gatb-core-cppunit were not linked against libdl.so.2 (they use none of the library's symbols) dh_installdeb -O--sourcedirectory=gatb-core dh_gencontrol -O--sourcedirectory=gatb-core dpkg-gencontrol: warning: Depends field of package libgatbcore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package gatb-core-testdata: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--sourcedirectory=gatb-core dh_builddeb -O--sourcedirectory=gatb-core dpkg-deb: building package 'gatb-core-dbgsym' in '../gatb-core-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_amd64.deb'. dpkg-deb: building package 'libgatbcore2' in '../libgatbcore2_1.4.1+git20181225.44d5a44+dfsg-3_amd64.deb'. dpkg-deb: building package 'gatb-core' in '../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_amd64.deb'. dpkg-deb: building package 'libgatbcore2-dbgsym' in '../libgatbcore2-dbgsym_1.4.1+git20181225.44d5a44+dfsg-3_amd64.deb'. dpkg-deb: building package 'libgatbcore-dev' in '../libgatbcore-dev_1.4.1+git20181225.44d5a44+dfsg-3_amd64.deb'. dpkg-deb: building package 'gatb-core-testdata' in '../gatb-core-testdata_1.4.1+git20181225.44d5a44+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gatb-core_1.4.1+git20181225.44d5a44+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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1990648/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1990648 and its subdirectories I: Current time: Tue Oct 3 18:16:46 +14 2023 I: pbuilder-time-stamp: 1696306606