Diff of the two buildlogs: -- --- b1/build.log 2022-08-30 21:45:34.097964070 +0000 +++ b2/build.log 2022-08-30 21:53:44.919651836 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 30 09:30:46 -12 2022 -I: pbuilder-time-stamp: 1661895046 +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 @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Jun 18 22:58:34 2019 -12 +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 @@ -36,136 +36,171 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2469149/tmp/hooks/D02_print_environment starting +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 - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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='775887ba472346a2868e4e791c001da1' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2469149' - PS1='# ' - PS2='> ' + 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' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.one4jv1ChI/pbuilderrc_kCCD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.one4jv1ChI/b1 --logfile b1/build.log gatb-core_1.4.1+git20181225.44d5a44+dfsg-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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 ionos11-amd64 5.10.0-17-amd64 #1 SMP Debian 5.10.136-1 (2022-08-13) x86_64 GNU/Linux + 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 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 6 20:23 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/2469149/tmp/hooks/D02_print_environment finished + -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 @@ -345,7 +380,7 @@ 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 2s (35.4 MB/s) +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.) @@ -887,7 +922,8 @@ 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 -I: Running cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gatb-core_1.4.1+git20181225.44d5a44+dfsg-3_source.changes +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 @@ -976,7 +1012,7 @@ 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 -j15 "INSTALL=install --strip-program=true" + 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 @@ -1001,46 +1037,68 @@ 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' -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 -[ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -[ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o -[ 2%] 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++ -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 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-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 -[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o -[ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -[ 4%] 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/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++ -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 -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 -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 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-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 -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 -[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o -[ 5%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -[ 5%] 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 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/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/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp make[4]: Entering directory 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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 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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 -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); @@ -1053,9 +1111,8 @@ 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: + 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); @@ -1067,12 +1124,15 @@ 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/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/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); @@ -1080,13 +1140,17 @@ /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); ^~~~~~~~~~ ~~ -[ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o /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/debruijn/impl/GraphUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp -In file included from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8: +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); @@ -1098,6 +1162,10 @@ 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, @@ -1116,13 +1184,23 @@ 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/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: + 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); @@ -1134,17 +1212,18 @@ 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=] -[ 7%] 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 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp +[ 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/Graph.cpp:20: + 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); @@ -1156,12 +1235,8 @@ 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-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 -[ 9%] 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 -[ 9%] 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 +[ 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, @@ -1179,16 +1254,12 @@ 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=] -[ 10%] 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 -[ 10%] 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 -[ 10%] 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 -[ 11%] 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 -[ 11%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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 +[ 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, @@ -1206,25 +1277,6 @@ 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=] -[ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.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 -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=] 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, @@ -1243,6 +1295,8 @@ 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, @@ -1260,14 +1314,24 @@ 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-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 -[ 13%] 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 -[ 13%] 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 -[ 14%] 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 +[ 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 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-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 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-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, @@ -1365,69 +1435,160 @@ 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=] -[ 17%] 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 -[ 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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 -[ 18%] 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 -[ 19%] 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 -[ 19%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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 -[ 19%] 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 -[ 19%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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/bank/impl/BankBinary.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp -[ 20%] 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 -[ 20%] 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 +[ 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 +[ 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-/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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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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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-O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o -c /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 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-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/Leon.hpp:33, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: + 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); @@ -1457,17 +1618,25 @@ 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=] -[ 26%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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/XmlReader.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp -[ 27%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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/Storage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp +/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/HeaderCoder.hpp:35, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: + 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); @@ -1479,8 +1648,52 @@ 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-static.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++ -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 +[ 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, @@ -1538,64 +1751,105 @@ /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/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]' + 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 non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] +/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/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 - ^~~~~~~~~~ -[ 28%] 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/BankConverterAlgorithm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp -/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); - ^~~~~~ ~~~~~ -[ 29%] 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 -[ 29%] 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/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/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]' + 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 non-trivial type 'class gatb::core::tools::math::NativeInt8'; use assignment or value-initialization instead [-Wclass-memaccess] +/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/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 - ^~~~~~~~~~ -[ 29%] 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/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, @@ -1611,12 +1865,35 @@ /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 ^~~~~~~~~~ -[ 30%] 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 -[ 30%] 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 -[ 31%] 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 +[ 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]': @@ -1627,10 +1904,6 @@ /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; ~~~~~^~~~~~~~~~~~~~~ -[ 31%] 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 -[ 31%] 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/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]': @@ -1641,6 +1914,28 @@ /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]': @@ -1651,20 +1946,18 @@ /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; ~~~~~^~~~~~~~~~~~~~~ -[ 32%] 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/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; - ~~~~~^~~~~~~~~~~~~~~ +[ 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_32.cpp:2: + 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); @@ -1677,7 +1970,7 @@ ^~~~~~~~~~~~~~~~~ ~~ /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_128.cpp:2: + 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); @@ -1689,22 +1982,21 @@ 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/bank/impl/BankFasta.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/BankFasta.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.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_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/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 +[ 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_96.cpp:2: + 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); @@ -1716,14 +2008,53 @@ 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_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++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); @@ -1731,29 +2062,16 @@ /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/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/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:12: warning: format '%llu' expects argument 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/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++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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_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]': @@ -1764,13 +2082,6 @@ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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]' @@ -1778,6 +2089,78 @@ /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 @@ -1791,17 +2174,79 @@ 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_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/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: @@ -1822,6 +2267,8 @@ /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, @@ -1835,39 +2282,10 @@ /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/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/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_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; - ^~~~~~~~~~~ +[ 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, @@ -1875,18 +2293,18 @@ 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]' + 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<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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_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 + 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, @@ -1896,7 +2314,7 @@ 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: + 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 @@ -1908,99 +2326,54 @@ 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: + 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/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/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: + 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/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: +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/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 - ^~~~~ -[ 32%] 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 -[ 33%] 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 -[ 33%] 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 -[ 33%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 -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/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]' + 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 type 'struct gatb::core::kmer::impl::Kmer<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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/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 - ^~~~~ -[ 33%] 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/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 @@ -2016,21 +2389,8 @@ /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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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 @@ -2049,50 +2409,44 @@ /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++) ~~^~~~~~~~~~~~~~~~~~~~~ -[ 34%] 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 -/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++) - ~~^~~~~~~~~~~~~~~~~~~~~ -[ 34%] 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 -[ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 -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/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: @@ -2116,19 +2470,6 @@ 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/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]' @@ -2139,50 +2480,10 @@ /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/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, @@ -2227,45 +2528,60 @@ /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 ^~~~~~~~~~~ -[ 36%] 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/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 +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] +/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] +/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] +/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: 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] +/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] +/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] +/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_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]': + 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++) @@ -2285,9 +2601,9 @@ 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]' + 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) @@ -2299,6 +2615,56 @@ 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: @@ -2316,35 +2682,181 @@ /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/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: + 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/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: +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/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: + 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 @@ -2352,16 +2864,21 @@ 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: + 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 ^~~~~~~~~~~ -[ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 +[ 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, @@ -2383,6 +2900,20 @@ /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 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-Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -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, @@ -2404,6 +2935,41 @@ /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 /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/XmlReader.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp +[ 58%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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/Storage.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp +[ 58%] Building CXX object src/CMakeFiles/gatbcore-static.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++ -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, @@ -2425,24 +2991,6 @@ /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 ^~~~~~~~~~ -[ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 -[ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 -[ 37%] 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 -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, @@ -2465,18 +3013,6 @@ /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]; ^~~~~~~~~ -[ 37%] 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/logging.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp -[ 38%] 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/bcalm2/ograph.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp -[ 38%] 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 -[ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.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++ -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 -[ 39%] 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 -[ 39%] 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 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, @@ -2493,59 +3029,26 @@ 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/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=] -[ 40%] 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 -[ 40%] 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 -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=] -[ 40%] 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 -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]; - ^~~~~~~~~ -[ 41%] 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/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, @@ -2562,34 +3065,28 @@ 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]; ^~~~~~~~~ -[ 42%] 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 -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=] -[ 42%] 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 +[ 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, @@ -2611,10 +3108,8 @@ 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: + 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); @@ -2626,6 +3121,14 @@ 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, @@ -2644,16 +3147,13 @@ 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=] -[ 43%] 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/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: + 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); @@ -2665,8 +3165,34 @@ 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=] -[ 43%] 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 +[ 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, @@ -2685,10 +3211,6 @@ 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=] -[ 43%] 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 -[ 43%] 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, @@ -2696,7 +3218,7 @@ 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: + 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); @@ -2708,10 +3230,8 @@ 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=] -[ 44%] 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 -[ 44%] 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 +[ 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, @@ -2719,18 +3239,18 @@ 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]' + 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<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<128>::Count' declared here + 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, @@ -2740,18 +3260,18 @@ 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]' + 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<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<96>::Count' declared here + 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, @@ -2761,22 +3281,20 @@ 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]' + 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<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<64>::Count' declared here + 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 ^~~~~ -[ 45%] 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, @@ -2784,7 +3302,7 @@ 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: + 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); @@ -2803,7 +3321,7 @@ 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: + 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 @@ -2813,10 +3331,35 @@ 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: + 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, @@ -2824,18 +3367,18 @@ 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]' + 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<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<96>::Count' declared here + 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, @@ -2845,18 +3388,18 @@ 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]' + 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<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<>::Count' declared here + 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, @@ -2866,7 +3409,7 @@ 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: + 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 @@ -2876,30 +3419,27 @@ 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: + 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 ^~~~~ -[ 45%] 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 -[ 45%] 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/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=] +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, @@ -2907,18 +3447,18 @@ 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]' + 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<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<>::Count' declared here + 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, @@ -2928,7 +3468,7 @@ 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: + 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 @@ -2938,7 +3478,7 @@ 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: + 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 ^~~~~ @@ -2949,28 +3489,7 @@ 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: + 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 @@ -2980,7 +3499,7 @@ 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: + 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 ^~~~~ @@ -3010,45 +3529,22 @@ 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]' + 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<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<128>::Count' declared here + 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/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/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: +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); @@ -3060,13 +3556,8 @@ 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_64.cpp:1: +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); @@ -3078,13 +3569,61 @@ 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/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: + 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); @@ -3092,10 +3631,50 @@ /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, @@ -3159,6 +3738,28 @@ /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, @@ -3180,15 +3781,13 @@ /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 ^~~~~ -[ 46%] 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: + 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); @@ -3203,78 +3802,216 @@ 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]' + 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<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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/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 +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/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: + 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/debruijn/impl/Graph.hpp:37, - from /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: +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/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]' + 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<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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<64>::Count' declared here +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/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]' + 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 type 'struct gatb::core::kmer::impl::Kmer<>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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/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 - ^~~~~ +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/TemplateSpecialization8.cpp.in_32.cpp:1: + 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); @@ -3286,8 +4023,8 @@ 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=] -[ 46%] 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 +[ 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, @@ -3295,7 +4032,7 @@ 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: + 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 @@ -3305,7 +4042,7 @@ 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: + 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 ^~~~~ @@ -3316,7 +4053,7 @@ 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: + 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 @@ -3326,7 +4063,7 @@ 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: + 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 ^~~~~ @@ -3337,7 +4074,7 @@ 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: + 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 @@ -3347,7 +4084,7 @@ 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: + 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 ^~~~~ @@ -3358,7 +4095,7 @@ 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: + 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 @@ -3368,10 +4105,46 @@ 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: + 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, @@ -3456,6 +4229,10 @@ /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, @@ -3540,6 +4317,42 @@ /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, @@ -3547,7 +4360,7 @@ 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: + 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 @@ -3557,7 +4370,7 @@ 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: + 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 ^~~~~ @@ -3568,7 +4381,7 @@ 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: + 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 @@ -3578,7 +4391,7 @@ 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: + 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 ^~~~~ @@ -3589,7 +4402,7 @@ 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: + 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 @@ -3599,7 +4412,7 @@ 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: + 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 ^~~~~ @@ -3610,7 +4423,7 @@ 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: + 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 @@ -3620,683 +4433,12 @@ 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/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=] -[ 47%] 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 -[ 47%] 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 -[ 47%] 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 -[ 48%] 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 -[ 48%] 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 -[ 48%] 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 -[ 50%] 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/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/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=] -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=] -[ 50%] 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 -[ 51%] 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 -[ 51%] 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 -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/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=] -[ 51%] 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 -[ 52%] 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 -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=] -[ 52%] 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 -[ 53%] 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 -[ 53%] 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 -[ 53%] 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 -[ 54%] 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 -[ 54%] 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 -[ 55%] 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 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-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 -[ 55%] 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 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-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 -[ 56%] 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 -[ 57%] 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 -[ 57%] 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 -[ 57%] 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 -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=] -[ 58%] 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 -[ 58%] 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 -[ 59%] 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 -[ 59%] 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 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-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 -[ 61%] 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 -/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 ) ; - ^~~ -[ 61%] 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 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-c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/src/gatb/tools/misc/api/Data.cpp -[ 64%] 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 -[ 64%] 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 -[ 65%] 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 -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/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/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/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/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 - ^~~~~~~~~~ -[ 65%] 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 -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: + 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 ^~~~~ -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 - ^~~~~~~~~~~ -[ 65%] 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 -[ 66%] 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 -[ 66%] 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 -[ 67%] 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 -[ 67%] 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 -[ 67%] 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 -[ 68%] 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 -[ 68%] 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 -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 - ^~~~~~~~~~ -[ 69%] 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 -[ 69%] 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 -[ 69%] 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/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/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_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_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; - ~~~~~^~~~~~~~~~~~~~~ -[ 70%] 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 -[ 70%] 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 -[ 71%] 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 -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/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); - ~~~~~~~~~~~~~~~ -[ 71%] 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/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_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=] -[ 71%] 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 -[ 72%] 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 -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/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/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/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/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/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); - ~~~~~~~~~~~~~~~ -[ 72%] 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/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++) -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); - ^~~~~~~~~~ ~~ -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; - ^~~~~~~~~~~ -/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/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++) - ~~^~~~~~~~~~~~~~~~~~~~~ +[ 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 @@ -4330,62 +4472,6 @@ /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: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; - ^~~~~~~~~~~ -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; - ~~~~~^~~~~~~~~~~~~~~ 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: @@ -4419,6 +4505,12 @@ /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, @@ -4426,20 +4518,21 @@ 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]' + 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<128>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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_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 + 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, @@ -4447,7 +4540,7 @@ 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: + 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 @@ -4459,109 +4552,74 @@ 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: + 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/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 +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] +/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] +/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] +/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++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - ^~~~~~~~~~~ -/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: 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] +/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] +/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] +/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_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/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]': + 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++) @@ -4581,9 +4639,9 @@ 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]' + 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) @@ -4591,26 +4649,39 @@ /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/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 - ^~~~~ -[ 73%] 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/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, @@ -4618,18 +4689,18 @@ 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]' + 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<64>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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_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 + 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, @@ -4639,7 +4710,7 @@ 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: + 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 @@ -4651,51 +4722,37 @@ 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: + 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 ^~~~~~~~~~~ -[ 73%] 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/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++) - ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] 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 -/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++) - ~~^~~~~~~~~~~~~~~~~~~~~ +[ 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_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]': + 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++) @@ -4715,9 +4772,9 @@ 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]' + 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) @@ -4725,6 +4782,8 @@ /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, @@ -4732,18 +4791,18 @@ 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]' + 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<96>::Count' with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] +/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_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 + 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, @@ -4753,7 +4812,7 @@ 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: + 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 @@ -4765,12 +4824,10 @@ 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: + 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 ^~~~~~~~~~~ -[ 75%] 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 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, @@ -4798,33 +4855,6 @@ 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 - ^~~~~~~~~~ -[ 75%] 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 -[ 76%] 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 -[ 76%] 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 -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]' @@ -4840,6 +4870,8 @@ /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, @@ -4861,10 +4893,12 @@ /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 ^~~~~~~~~~ -[ 77%] 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 CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o 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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, @@ -4881,6 +4915,16 @@ 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, @@ -4897,34 +4941,6 @@ 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/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]; - ^~~~~~~~~ -/usr/bin/ranlib ../lib/None/libgatbcore.a -make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target gatbcore-static -make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.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/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= -Scanning dependencies of target gatb-core-cppunit -make[4]: 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[4]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.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/TestBank.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp -[ 77%] 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 -[ 78%] 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 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, @@ -4941,6 +4957,12 @@ 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 @@ -4969,8 +4991,6 @@ /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]; ^~~~~~~~~ -[ 78%] 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/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, @@ -4989,14 +5009,16 @@ 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=] -[ 79%] 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 -[ 79%] 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 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-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 -[ 80%] 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 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-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, @@ -5015,8 +5037,6 @@ 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 test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.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 /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestLeon.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, @@ -5035,8 +5055,8 @@ 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-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 +[ 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, @@ -5055,10 +5075,27 @@ 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=] -[ 82%] 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 -[ 82%] 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 +[ 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, @@ -5078,10 +5115,8 @@ 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-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 -[ 83%] 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 +[ 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, @@ -5103,25 +5138,6 @@ /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/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, @@ -5189,9 +5205,10 @@ 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: + 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); @@ -5203,10 +5220,8 @@ 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-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 -[ 84%] 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 +[ 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, @@ -5226,16 +5241,13 @@ 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-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/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: + 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); @@ -5310,8 +5322,47 @@ /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 ^~~~~ -[ 85%] 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 +[ 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, @@ -5333,24 +5384,6 @@ /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/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, @@ -5477,81 +5510,8 @@ /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_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/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/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/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=] +[ 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, @@ -5579,7 +5539,7 @@ 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: + 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); @@ -5597,7 +5557,7 @@ 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: + 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); @@ -5609,8 +5569,6 @@ 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%] Building CXX object 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/TestSequence.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bank/TestSequence.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, @@ -5695,6 +5653,8 @@ /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, @@ -5702,7 +5662,7 @@ 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: + 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 @@ -5712,7 +5672,7 @@ 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: + 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 ^~~~~ @@ -5723,7 +5683,7 @@ 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: + 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 @@ -5733,7 +5693,7 @@ 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: + 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 ^~~~~ @@ -5744,7 +5704,7 @@ 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: + 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 @@ -5754,7 +5714,7 @@ 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: + 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 ^~~~~ @@ -5765,7 +5725,7 @@ 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: + 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 @@ -5775,10 +5735,52 @@ 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: + 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, @@ -5786,7 +5788,7 @@ 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: + 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 @@ -5796,7 +5798,7 @@ 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: + 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 ^~~~~ @@ -5807,7 +5809,7 @@ 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: + 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 @@ -5817,7 +5819,7 @@ 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: + 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 ^~~~~ @@ -5828,7 +5830,7 @@ 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: + 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 @@ -5838,7 +5840,7 @@ 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: + 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 ^~~~~ @@ -5849,7 +5851,7 @@ 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: + 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 @@ -5859,7 +5861,7 @@ 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: + 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 ^~~~~ @@ -5870,7 +5872,7 @@ 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: + 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 @@ -5880,7 +5882,7 @@ 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: + 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 ^~~~~ @@ -5891,7 +5893,7 @@ 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: + 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 @@ -5901,7 +5903,7 @@ 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: + 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 ^~~~~ @@ -5912,7 +5914,7 @@ 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: + 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 @@ -5922,7 +5924,7 @@ 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: + 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 ^~~~~ @@ -5933,7 +5935,7 @@ 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: + 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 @@ -5943,35 +5945,18 @@ 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: + 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 ^~~~~ -[ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.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/bcalm/TestBcalm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp -[ 86%] 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 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-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, @@ -6008,13 +5993,85 @@ 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=] -[ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o +[ 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 CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o 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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/bcalm/TestBcalm.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.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 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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/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 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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/debruijn/TestSimplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.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/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/test/unit/src/debruijn/TestDebruijn.cpp:33: + 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); @@ -6047,7 +6104,7 @@ 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: + 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); @@ -6059,35 +6116,12 @@ 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=] -[ 89%] Linking CXX executable ../bin/None/dbginfo -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -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/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm -make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 89%] Built target dbginfo -make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.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/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= -Scanning dependencies of target dbgh5 -make[4]: Leaving 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/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/tools/leon.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: + 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); @@ -6104,7 +6138,8 @@ 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: + 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); @@ -6116,25 +6151,10 @@ 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()); - ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.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/debruijn/TestSimplifications.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp -[ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.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/debruijn/TestSimplificationsUnitigs.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp -[ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.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/TestDSK.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp -[ 92%] 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 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: + 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); @@ -6146,9 +6166,6 @@ 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=] -[ 93%] Linking CXX executable ../bin/None/leon -cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -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 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, @@ -6165,10 +6182,47 @@ 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' -[ 93%] Built target leon -[ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.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/TestDebloom.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.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/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, @@ -6188,37 +6242,21 @@ /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 ^~~~~ -[ 93%] 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 -[ 94%] 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 -make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target dbgh5 -[ 94%] 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 -[ 95%] 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 -[ 95%] 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 -[ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o +[ 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 CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp +[ 94%] Linking CXX executable ../bin/None/dbginfo +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -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/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm +[ 95%] Linking CXX executable ../bin/None/leon +cd /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -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 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.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/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=] +make[4]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target leon [ 96%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.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/TestContainer.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/collections/TestContainer.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o @@ -6227,6 +6265,12 @@ 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 /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/math/TestMath.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp +[ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o +cd /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: @@ -6241,12 +6285,10 @@ 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=] -[ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.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/math/TestMath.cpp.o -c /build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp -[ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -cd /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 +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, @@ -6266,12 +6308,6 @@ /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 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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 CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o 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CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/api/Data.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o 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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' -[100%] Built target gatbcore-dynamic make[3]: 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[2]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' @@ -6288,7 +6324,7 @@ 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 -j15 install DESTDIR=/build/gatb-core-1.4.1\+git20181225.44d5a44\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + 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 @@ -6305,59 +6341,59 @@ 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 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/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[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 0%] Built target thirdparty_copy make[3]: 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[3]: 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 +[ 0%] Built target thirdparty_copy make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-static.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-dynamic.dir/build'. +make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' [ 43%] Built target gatbcore-static make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend +[ 86%] Built target gatbcore-dynamic 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/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/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]: 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 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tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.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 && /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 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'/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-dynamic.dir/build'. +make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/leon.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' +[ 87%] Built target dbgh5 make[3]: Entering directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/unit/CMakeFiles/gatb-core-cppunit.dir/build'. make[3]: Leaving directory '/build/gatb-core-1.4.1+git20181225.44d5a44+dfsg/obj-x86_64-linux-gnu' -[ 44%] Built target dbgh5 -[ 45%] Built target dbginfo -[ 88%] Built target gatbcore-dynamic +[ 89%] Built 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' @@ -6764,7 +6800,7 @@ 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-gensymbolsa78nte 2022-08-30 09:44:08.292673269 -1200 ++++ 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 @@ -6782,19 +6818,19 @@ _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 H5Aread used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzflush used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Pset_chunk used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5T_NATIVE_UINT64_g used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Pset_shuffle used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol inflate used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Pcreate used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries +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 H5Dget_space used by debian/libgatbcore2/usr/lib/x86_64-linux-gnu/libgatbcore.so.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Gcreate2 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/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/dbginfo were not linked against libdl.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/lib/gatb-core/gatb-core-cppunit debian/gatb-core/usr/bin/dbgh5 debian/gatb-core/usr/bin/dbginfo 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 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 @@ -6803,8 +6839,8 @@ 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 'libgatbcore2-dbgsym' in '../libgatbcore2-dbgsym_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 @@ -6814,12 +6850,14 @@ 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/2469149 and its subdirectories -I: Current time: Tue Aug 30 09:45:33 -12 2022 -I: pbuilder-time-stamp: 1661895933 +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