Diff of the two buildlogs: -- --- b1/build.log 2020-12-08 18:32:33.103284120 +0000 +++ b2/build.log 2020-12-08 18:35:02.297341522 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 10 12:52:41 -12 2022 -I: pbuilder-time-stamp: 1641862361 +I: Current time: Wed Dec 9 08:32:35 +14 2020 +I: pbuilder-time-stamp: 1607452355 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 Mon Jan 7 23:57:26 2019 -12 +gpgv: Signature made Wed Jan 9 01:57:26 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking kissplice_2.4.0-p1-4.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16685/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/55932/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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' +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/55932/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/55932/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=16' - 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=15' + 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='0f8adf3572f149a5849de6321ab10b1d' - 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='16685' - PS1='# ' - PS2='> ' + INVOCATION_ID=704d8b0530a34e8d8a5f13a2bb660103 + 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=55932 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.ALcdiNRK4z/pbuilderrc_yGc1 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ALcdiNRK4z/b1 --logfile b1/build.log kissplice_2.4.0-p1-4.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://85.184.249.68:3128' + 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.ALcdiNRK4z/pbuilderrc_W82W --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ALcdiNRK4z/b2 --logfile b2/build.log kissplice_2.4.0-p1-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.9.0-0.bpo.2-amd64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) 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 Jan 9 02:47 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/16685/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 Dec 9 08:32 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 7 22:24 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/55932/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -291,7 +325,7 @@ Get: 89 http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 [1212 B] Get: 90 http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 [1192 B] Get: 91 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 71.1 MB in 1s (64.9 MB/s) +Fetched 71.1 MB in 2s (40.5 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.) @@ -683,7 +717,7 @@ 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/kissplice-2.4.0-p1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/kissplice-2.4.0-p1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.4.0-p1-4 dpkg-buildpackage: info: source distribution unstable @@ -727,7 +761,7 @@ -- Build files have been written to: /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/kissplice-2.4.0-p1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-2.4.0-p1 -B/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -737,94 +771,91 @@ make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/debruijn-v4 /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4/CMakeFiles/ks_debruijn4.dir/DependInfo.cmake --color= -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/thirdparty/kissreads/src /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake --color= +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/thirdparty/kissreads/src /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend +make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend -Scanning dependencies of target ks_debruijn4 -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake --color= -make -f debruijn-v4/CMakeFiles/ks_debruijn4.dir/build.make debruijn-v4/CMakeFiles/ks_debruijn4.dir/build make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend -make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +Scanning dependencies of target ks_kissreadsSplice +make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +Scanning dependencies of target ks_debruijn4 +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.4.0-p1 /build/kissplice-2.4.0-p1/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake --color= -Scanning dependencies of target ks_kissreadsSplice +make -f debruijn-v4/CMakeFiles/ks_debruijn4.dir/build.make debruijn-v4/CMakeFiles/ks_debruijn4.dir/build +Scanning dependencies of target ks_clean_duplicates make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -Scanning dependencies of target ks_kissreadsSNPS +make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build -Scanning dependencies of target ks_clean_duplicates +Scanning dependencies of target ks_kissreadsSNPS make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +Scanning dependencies of target ks_run_modules +Scanning dependencies of target ks_bubble_enumeration make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build -Scanning dependencies of target ks_bubble_enumeration -make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -Scanning dependencies of target ks_run_modules -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 1%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/main.cpp.o make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' Scanning dependencies of target ks_print_bcc +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build -[ 2%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Bloom.cpp.o Scanning dependencies of target ks_error_removal make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/main.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/main.cpp make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build -[ 3%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Bank.cpp.o -[ 5%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Pool.cpp.o -[ 6%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.c.o -make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/commons.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/commons.c -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Pool.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Pool.cpp -[ 7%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build -[ 8%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o -[ 10%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Hash16.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/commons.c -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Bank.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bank.cpp -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/extension_algorithm.c +[ 1%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Pool.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Pool.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Pool.cpp make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 11%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o -[ 12%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/interface_libchash.c -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/kissplice-2.4.0-p1/modules/CleanDuplicates.cpp -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Bloom.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Hash16.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Hash16.cpp -[ 13%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o -[ 15%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Kmer.cpp.o +make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +[ 2%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o +[ 3%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Bank.cpp.o +[ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Bank.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bank.cpp +[ 6%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/main.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/commons.c +[ 7%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.c.o +[ 8%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/extension_algorithm.c -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Kmer.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Kmer.cpp -[ 16%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/commons.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/commons.c +[ 10%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/kissplice-2.4.0-p1/modules/run.cpp +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/kissplice-2.4.0-p1/modules/CleanDuplicates.cpp +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/main.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/main.cpp +[ 11%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Bloom.cpp.o +[ 12%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o +[ 13%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.cpp +[ 15%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/extension_algorithm.c +[ 16%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/interface_libchash.c +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Bloom.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/interface_libchash.c [ 17%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -[ 18%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -[ 20%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -c /build/kissplice-2.4.0-p1/modules/ErrorRemoval.cpp +[ 18%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/kissplice-2.4.0-p1/modules/PrintBcc.cpp -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/kissplice-2.4.0-p1/modules/run.cpp -[ 21%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o +[ 20%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c -[ 22%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/outputs.c +[ 21%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c: In function 'HashFind': /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -835,6 +866,7 @@ /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:1221:4: note: in expansion of macro 'LOAD_AND_RETURN' LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); ^~~~~~~~~~~~~~~ +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c: In function 'HashFindLast': /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -915,29 +947,10 @@ /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:627:3: note: in expansion of macro 'READ_UL' READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); ^~~~~~~ -[ 24%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o -[ 25%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/interface_libchash.c -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/coherent_algorithm.c -[ 26%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/couple.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/couple.c -[ 27%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/fragment_index.c -[ 29%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Set.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Set.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp: In member function 'void Bloom::load(char*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp:256:9: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - printf("loading bloom filter from file, nelem %lli \n",nchar); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -[ 30%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Utils.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Utils.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp:257:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(blooma, sizeof(unsigned char), nchar, file_data); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c -[ 32%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/SortingCount.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/SortingCount.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp +[ 22%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/outputs.c +[ 24%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/outputs.c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c: In function 'HashFind': /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -1028,12 +1041,8 @@ /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/libchash.c:627:3: note: in expansion of macro 'READ_UL' READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); ^~~~~~~ -In file included from /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.cpp:61: -/build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h:124:1: warning: 'typedef' was ignored in this declaration - typedef struct Path { - ^~~~~~~ -[ 34%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/kissReads.c +[ 25%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/coherent_algorithm.c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bank.cpp: In member function 'void Bank::init(char**, int)': /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bank.cpp:279:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] strerror_r( errno, buffer, BUFSIZ ); // get string message from errno @@ -1050,12 +1059,43 @@ /build/kissplice-2.4.0-p1/debruijn-v4/minia/Bank.cpp:985:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof( char),block_size, binary_read_file); // read a block of sequences into the buffer ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp: In member function 'void Bloom::load(char*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp:256:9: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + printf("loading bloom filter from file, nelem %lli \n",nchar); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +[ 26%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/coherent_algorithm.c +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Bloom.cpp:257:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(blooma, sizeof(unsigned char), nchar, file_data); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 27%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp: In function 'void construct_linear_seqs()': +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:105:55: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] + if ((NbBranchingKmer%300)==0) fprintf (stderr,"%cLooping through branching kmer n° %lld / %lld ",13,NbBranchingKmer,terminator->nb_branching_kmers); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:105:55: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'int64_t' {aka 'long int'} [-Wformat=] +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp: In function 'int main(int, char**)': +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:177:20: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] + printf("Max kmer size on this compiled version is %d\n",sizeof(kmer_type)*4-2); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:206:15: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + printf("estimated values: nbits Bloom %i, nb FP %lld, max memory %i MB\n",estimated_bloom_size,estimated_nb_FP,max_memory); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ +[ 29%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/couple.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/couple.c +In file included from /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.cpp:61: +/build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h:124:1: warning: 'typedef' was ignored in this declaration + typedef struct Path { + ^~~~~~~ +[ 30%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/couple.c +[ 31%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Hash16.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Hash16.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Hash16.cpp In file included from /build/kissplice-2.4.0-p1/modules/PrintBcc.cpp:51: /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h:124:1: warning: 'typedef' was ignored in this declaration typedef struct Path { ^~~~~~~ -[ 35%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/list.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/list.c In file included from /build/kissplice-2.4.0-p1/modules/PrintBcc.cpp:51: /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = Printer; TNodeFunctor = Printer]': /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] @@ -1096,26 +1136,28 @@ /build/kissplice-2.4.0-p1/modules/CGraph.h:339:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/LinearCounter.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/LinearCounter.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/LinearCounter.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:56:15: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] - getcwd(current_path,sizeof(current_path)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:283:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system("echo 3 > /proc/sys/vm/drop_caches"); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:537:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system("echo 3 > /proc/sys/vm/drop_caches"); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp: In member function 'void AssocPairedSet::load(char*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp:290:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:434:112: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] - if ((NbRead%10000)==0) fprintf (stderr,(char*)"%cExtrapolating number of distinct kmers %lld",13,NbRead); - ~~~~~~^ +[ 34%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/fragment_index.c +[ 34%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/fragment_index.c +[ 35%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/kissReads.c +[ 36%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp +[ 37%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/list.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/list.c +[ 39%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Kmer.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Kmer.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Kmer.cpp +[ 40%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Set.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Set.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp +[ 41%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/kissReads.c +[ 43%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/tree.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/tree.c +[ 44%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/CEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp +[ 45%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/tree.c In file included from /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.cpp:61: /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': /build/kissplice-2.4.0-p1/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] @@ -1159,28 +1201,65 @@ /build/kissplice-2.4.0-p1/modules/CGraph.h:294:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, 100 * MAX, edge_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp: In function 'void construct_linear_seqs()': -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:105:55: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] - if ((NbBranchingKmer%300)==0) fprintf (stderr,"%cLooping through branching kmer n° %lld / %lld ",13,NbBranchingKmer,terminator->nb_branching_kmers); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:105:55: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'int64_t' {aka 'long int'} [-Wformat=] -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp: In function 'int main(int, char**)': -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:177:20: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] - printf("Max kmer size on this compiled version is %d\n",sizeof(kmer_type)*4-2); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/main.cpp:206:15: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - printf("estimated values: nbits Bloom %i, nb FP %lld, max memory %i MB\n",estimated_bloom_size,estimated_nb_FP,max_memory); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ +[ 46%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.c.o +[ 48%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/list.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/list.c +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp +[ 49%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp +[ 50%] Linking C executable ../../../lib/kissplice/ks_kissreadsSplice +[ 51%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 +[ 53%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp +[ 54%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSplice.dir/commons.c.o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o CMakeFiles/ks_kissreadsSplice.dir/couple.c.o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o CMakeFiles/ks_kissreadsSplice.dir/list.c.o CMakeFiles/ks_kissreadsSplice.dir/tree.c.o -o ../../../lib/kissplice/ks_kissreadsSplice -lm -lz +[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp: In member function 'void AssocPairedSet::load(char*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Set.cpp:290:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 56%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp +[ 58%] Linking CXX executable ../lib/kissplice/ks_print_bcc +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 +[ 59%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Utils.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Utils.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp +[ 60%] Linking C executable ../../../lib/kissplice/ks_kissreadsSNPS +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/kissplice/ks_print_bcc +[ 60%] Built target ks_kissreadsSplice +[ 62%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/SortingCount.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/SortingCount.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o CMakeFiles/ks_kissreadsSNPS.dir/list.c.o CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -o ../../../lib/kissplice/ks_kissreadsSNPS -lm -lz +[ 63%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp +[ 64%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +[ 64%] Built target ks_kissreadsSNPS +[ 64%] Built target ks_print_bcc +[ 65%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp +[ 67%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp +[ 68%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:434:112: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] + if ((NbRead%10000)==0) fprintf (stderr,(char*)"%cExtrapolating number of distinct kmers %lld",13,NbRead); + ~~~~~~^ /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp: In instantiation of 'Bloom* bloom_create_bloo1(T*, bool) [with T = BloomCpt]': /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:167:85: required from here /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:121:16: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("load bloom from dump, containing %lli solid kmers b1_size %lli\n",nsolids,b1_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~ /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:121:16: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] -[ 37%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Debloom.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Debloom.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp -[ 39%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/tree.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/tree.c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp: In function 'void end_kmer_count_partition(bool, Hash16*)': /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:187:14: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_write), 0); //erase previous file @@ -1191,20 +1270,6 @@ /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:225:18: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_read), 0); //erase previous file ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:45:24: warning: '%s' directive writing up to 1023 bytes into a region of size 512 [-Wformat-overflow=] - sprintf(p_buf, "%s/%s", temp_dir, ep->d_name); - ^~~~~~~ ~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.h:1, - from /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:1: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 1280 bytes into a destination of size 512 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp: In function 'char* return_file_name(const char*)': /build/kissplice-2.4.0-p1/debruijn-v4/minia/Utils.cpp:28:26: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(fileName,"%s.%s",prefix,suffix); @@ -1217,110 +1282,43 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp -[ 43%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/outputs.c -[ 44%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp -[ 45%] Linking C executable ../../../lib/kissplice/ks_kissreadsSplice -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSplice.dir/commons.c.o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o CMakeFiles/ks_kissreadsSplice.dir/couple.c.o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o CMakeFiles/ks_kissreadsSplice.dir/list.c.o CMakeFiles/ks_kissreadsSplice.dir/tree.c.o -o ../../../lib/kissplice/ks_kissreadsSplice -lm -lz -[ 46%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Traversal.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Traversal.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Traversal.cpp -[ 48%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 48%] Built target ks_kissreadsSplice -[ 49%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/coherent_algorithm.c -[ 50%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/couple.c -[ 51%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Terminator.cpp.o -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'int debloom(int, int)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:154:53: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - if ((NbSolidKmer%10000)==0) fprintf (stderr,"%c Writing positive Bloom Kmers %lld",13,NbSolidKmer); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Terminator.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:158:20: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr,"\n%lli kmers written\n",cc); - ^~~~~~~~~~~~~~~~~~~~~~~~ ~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:191:53: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - if ((NbSolidKmer%10000)==0) fprintf (stderr,"%cBuild Hash table %lld",13,NbSolidKmer); - ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:195:28: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr,"End of debloom partition %lli / %lld \n",hasht1->nb_elem,max_kmer_per_part); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:195:28: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:208:28: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr,"\n%lli false positives written , partition %i \n",n_false_positives,numpart); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:225:20: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr,"Total nb false positives stored in the Debloom hashtable %lli \n",n_false_positives); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'Set* load_false_positives()': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:280:133: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] - if ((NbInsertedKmers%10000)==0) fprintf (stderr,(char*)"%cInsert false positive Kmers in hash table %lld",13,NbInsertedKmers); - ~~~~~~~~~~~~~~~^ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:284:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - fprintf (stderr,"\nInserted %lld false positive kmers in the hash structure.\n\n",NbInsertedKmers); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void print_size_summary(FPSet*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:445:19: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr, "Size of the FP table : %lli FP x %d bits = %.2lf MB \n", fp->capacity(), bits_per_FP_element, toMB((double)(size_T1)) ); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:448:18: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void print_size_summary(FPSetCascading4*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:465:18: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -[ 53%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/OAHash.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/OAHash.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/OAHash.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void end_debloom_partition(bool)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:29:11: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] - ftruncate(fileno(F_debloom_write), 0); //erase previous file - ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/GraphOutput.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/GraphOutput.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp -[ 55%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/kissplice-2.4.0-p1/modules/CycleCompression.cpp -[ 56%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/fragment_index.c -[ 58%] Linking CXX executable ../lib/kissplice/ks_print_bcc -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/kissplice/ks_print_bcc -[ 59%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp -[ 60%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/kissReads.c -[ 62%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp -[ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp +[ 69%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/LinearCounter.cpp.o +/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:56:15: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] + getcwd(current_path,sizeof(current_path)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:283:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system("echo 3 > /proc/sys/vm/drop_caches"); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:537:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system("echo 3 > /proc/sys/vm/drop_caches"); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/LinearCounter.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/LinearCounter.cpp +[ 70%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NNode.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp +[ 72%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp +[ 73%] Linking CXX executable ../lib/kissplice/ks_error_removal +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o CMakeFiles/ks_error_removal.dir/CEdge.cpp.o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -o ../lib/kissplice/ks_error_removal +[ 74%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:45:24: warning: '%s' directive writing up to 1023 bytes into a region of size 512 [-Wformat-overflow=] + sprintf(p_buf, "%s/%s", temp_dir, ep->d_name); + ^~~~~~~ ~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.h:1, + from /build/kissplice-2.4.0-p1/debruijn-v4/minia/SortingCount.cpp:1: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 1280 bytes into a destination of size 512 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 63%] Built target ks_print_bcc -[ 64%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/CEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp -[ 65%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/list.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/list.c -[ 67%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp -[ 68%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/build/kissplice-2.4.0-p1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -c /build/kissplice-2.4.0-p1/thirdparty/kissreads/src/tree.c -[ 69%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp -[ 70%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp -[ 72%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp -[ 73%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp -[ 74%] Linking C executable ../../../lib/kissplice/ks_kissreadsSNPS -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 -[ 75%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o CMakeFiles/ks_kissreadsSNPS.dir/list.c.o CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -o ../../../lib/kissplice/ks_kissreadsSNPS -lm -lz +[ 77%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Debloom.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Debloom.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp /build/kissplice-2.4.0-p1/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1050:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); @@ -1353,50 +1351,7 @@ /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1112:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, 100 * MAX, data_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 75%] Built target ks_kissreadsSNPS -[ 77%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp -[ 78%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, uint64_t, Bloom*, Set*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:275:29: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - fprintf (stderr,"%cExtrapolating the number of branching kmers from the first %dM kmers: %lld",13,(int)ceilf(nb_extrapolation/1024.0/1024.0),estimated_nb_branching_kmers); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:303:58: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] - if ((nb_branching_kmers%500)==0) fprintf (stderr,"%cIndexing branching kmers %lld / ~%lld",13,nb_branching_kmers,estimated_nb_branching_kmers); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:303:58: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, BinaryBank*, Bloom*, Set*)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:337:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] - fprintf (stderr,"\nLoaded %lld branching kmers x %lu B = %.1f MB\n",nb_branching_kmers,sizeof(cell),((1<)*1.0)/1024.0/1024.0); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NNode.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In constructor 'GraphOutput::GraphOutput(std::__cxx11::string, int, std::id_els)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:61:10: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - printf("graph_format=%d first_id_nodes=%d first_id_edges=%d\n", graph_format, first_id_els.node, first_id_els.edge); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:61:10: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In constructor 'GraphOutput::GraphOutput(std::__cxx11::string, int)': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:73:10: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - printf("graph_format=%d first_id_nodes=%d first_id_edges=%d\n", graph_format, first_id_els.node, first_id_els.edge); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:73:10: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In member function 'void GraphOutput::close()': -/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:108:49: warning: format '%s' expects a matching 'char*' argument [-Wformat=] - if(!edges || !nodes){fprintf(stderr,"Cannot open file %s, %s or %s, exit\n", json_edges_file_suffix.c_str(), json_nodes_file_suffix.c_str()); exit(1);} - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp -[ 82%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp -[ 83%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp -[ 84%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp -[ 86%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp +[ 77%] Built target ks_error_removal /build/kissplice-2.4.0-p1/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1050:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); @@ -1429,20 +1384,88 @@ /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1112:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, 100 * MAX, data_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp -[ 88%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp -[ 89%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp -[ 91%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/kissplice-2.4.0-p1/modules/SplitBcc.cpp -[ 92%] Linking CXX executable ../lib/kissplice/ks_error_removal -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 -[ 93%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o +[ 78%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp -[ 94%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +[ 79%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/kissplice-2.4.0-p1/modules/SplitBcc.cpp +[ 81%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Traversal.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Traversal.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Traversal.cpp +[ 82%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp +[ 83%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/Terminator.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/Terminator.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp +[ 84%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/OAHash.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/OAHash.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/OAHash.cpp +[ 86%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/NGraph.cpp +[ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/kissplice-2.4.0-p1/modules/CGraph.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, uint64_t, Bloom*, Set*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:275:29: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf (stderr,"%cExtrapolating the number of branching kmers from the first %dM kmers: %lld",13,(int)ceilf(nb_extrapolation/1024.0/1024.0),estimated_nb_branching_kmers); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:303:58: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] + if ((nb_branching_kmers%500)==0) fprintf (stderr,"%cIndexing branching kmers %lld / ~%lld",13,nb_branching_kmers,estimated_nb_branching_kmers); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:303:58: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, BinaryBank*, Bloom*, Set*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Terminator.cpp:337:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + fprintf (stderr,"\nLoaded %lld branching kmers x %lu B = %.1f MB\n",nb_branching_kmers,sizeof(cell),((1<)*1.0)/1024.0/1024.0); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/CEdge.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'int debloom(int, int)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:154:53: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + if ((NbSolidKmer%10000)==0) fprintf (stderr,"%c Writing positive Bloom Kmers %lld",13,NbSolidKmer); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:158:20: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr,"\n%lli kmers written\n",cc); + ^~~~~~~~~~~~~~~~~~~~~~~~ ~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:191:53: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + if ((NbSolidKmer%10000)==0) fprintf (stderr,"%cBuild Hash table %lld",13,NbSolidKmer); + ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:195:28: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr,"End of debloom partition %lli / %lld \n",hasht1->nb_elem,max_kmer_per_part); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:195:28: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:208:28: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr,"\n%lli false positives written , partition %i \n",n_false_positives,numpart); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:225:20: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr,"Total nb false positives stored in the Debloom hashtable %lli \n",n_false_positives); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'Set* load_false_positives()': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:280:133: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] + if ((NbInsertedKmers%10000)==0) fprintf (stderr,(char*)"%cInsert false positive Kmers in hash table %lld",13,NbInsertedKmers); + ~~~~~~~~~~~~~~~^ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:284:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=] + fprintf (stderr,"\nInserted %lld false positive kmers in the hash structure.\n\n",NbInsertedKmers); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void print_size_summary(FPSet*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:445:19: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr, "Size of the FP table : %lli FP x %d bits = %.2lf MB \n", fp->capacity(), bits_per_FP_element, toMB((double)(size_T1)) ); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:448:18: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void print_size_summary(FPSetCascading4*)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:465:18: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +[ 89%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/LabelledCEdge.cpp +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp: In function 'void end_debloom_partition(bool)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/Debloom.cpp:29:11: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] + ftruncate(fileno(F_debloom_write), 0); //erase previous file + ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o -c /build/kissplice-2.4.0-p1/modules/NNode.cpp +[ 92%] Building CXX object debruijn-v4/CMakeFiles/ks_debruijn4.dir/minia/GraphOutput.cpp.o +[ 93%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/c++ -Dkmer_type=__uint128_t -I/build/kissplice-2.4.0-p1/debruijn-v4 -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_debruijn4.dir/minia/GraphOutput.cpp.o -c /build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o -c /build/kissplice-2.4.0-p1/modules/NEdge.cpp +[ 94%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/build/kissplice-2.4.0-p1/modules -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/kissplice-2.4.0-p1/modules/Utils.cpp /build/kissplice-2.4.0-p1/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1050:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); @@ -1475,24 +1498,35 @@ /build/kissplice-2.4.0-p1/modules/NGraph.cpp:1112:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, 100 * MAX, data_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o CMakeFiles/ks_error_removal.dir/CEdge.cpp.o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -o ../lib/kissplice/ks_error_removal -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 94%] Built target ks_error_removal +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In constructor 'GraphOutput::GraphOutput(std::__cxx11::string, int, std::id_els)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:61:10: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + printf("graph_format=%d first_id_nodes=%d first_id_edges=%d\n", graph_format, first_id_els.node, first_id_els.edge); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:61:10: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In constructor 'GraphOutput::GraphOutput(std::__cxx11::string, int)': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:73:10: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + printf("graph_format=%d first_id_nodes=%d first_id_edges=%d\n", graph_format, first_id_els.node, first_id_els.edge); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:73:10: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp: In member function 'void GraphOutput::close()': +/build/kissplice-2.4.0-p1/debruijn-v4/minia/GraphOutput.cpp:108:49: warning: format '%s' expects a matching 'char*' argument [-Wformat=] + if(!edges || !nodes){fprintf(stderr,"Cannot open file %s, %s or %s, exit\n", json_edges_file_suffix.c_str(), json_nodes_file_suffix.c_str()); exit(1);} + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable ../lib/kissplice/ks_debruijn4 cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/debruijn-v4 && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_debruijn4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_debruijn4.dir/main.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Pool.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Bank.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Bloom.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Hash16.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Kmer.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Set.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Utils.cpp.o CMakeFiles/ks_debruijn4.dir/minia/SortingCount.cpp.o CMakeFiles/ks_debruijn4.dir/minia/LinearCounter.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Debloom.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Traversal.cpp.o CMakeFiles/ks_debruijn4.dir/minia/Terminator.cpp.o CMakeFiles/ks_debruijn4.dir/minia/OAHash.cpp.o CMakeFiles/ks_debruijn4.dir/minia/GraphOutput.cpp.o -o ../lib/kissplice/ks_debruijn4 -lz make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' [ 96%] Built target ks_debruijn4 -[ 97%] Linking CXX executable ../lib/kissplice/ks_run_modules -cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/CEdge.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/NNode.cpp.o CMakeFiles/ks_run_modules.dir/NEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/kissplice/ks_run_modules -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 97%] Built target ks_run_modules -[ 98%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration +[ 97%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/kissplice/ks_bubble_enumeration make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 98%] Built target ks_bubble_enumeration +[ 97%] Built target ks_bubble_enumeration +[ 98%] Linking CXX executable ../lib/kissplice/ks_run_modules +cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/CEdge.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/NNode.cpp.o CMakeFiles/ks_run_modules.dir/NEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/kissplice/ks_run_modules +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +[ 98%] Built target ks_run_modules [100%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates cd /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.4.0-p1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/kissplice/ks_clean_duplicates @@ -1502,10 +1536,10 @@ /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=-j16 + cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=-j15 make[1]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process -j16 +/usr/bin/ctest --force-new-ctest-process -j15 Test project /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu Start 1: KisspliceBasicTest Start 2: KisspliceDBGTest @@ -1515,18 +1549,18 @@ Start 6: ksBubbleEnumerationTest Start 7: ksRunModulesTest Start 8: ksErrorRemovalTest -1/8 Test #1: KisspliceBasicTest ............... Passed 0.11 sec -2/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.08 sec -3/8 Test #7: ksRunModulesTest ................. Passed 0.09 sec -4/8 Test #8: ksErrorRemovalTest ............... Passed 0.16 sec -5/8 Test #5: KisspliceGraphTest ............... Passed 5.20 sec -6/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 6.61 sec -7/8 Test #3: KisspliceTwoSequencesTest ........ Passed 41.48 sec -8/8 Test #2: KisspliceDBGTest ................. Passed 44.29 sec +1/8 Test #1: KisspliceBasicTest ............... Passed 0.13 sec +2/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.14 sec +3/8 Test #7: ksRunModulesTest ................. Passed 0.14 sec +4/8 Test #8: ksErrorRemovalTest ............... Passed 0.17 sec +5/8 Test #5: KisspliceGraphTest ............... Passed 4.07 sec +6/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 5.03 sec +7/8 Test #3: KisspliceTwoSequencesTest ........ Passed 26.36 sec +8/8 Test #2: KisspliceDBGTest ................. Passed 35.85 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 44.30 sec +Total Test time (real) = 35.86 sec make[1]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -1534,7 +1568,7 @@ dh_testroot dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/kissplice-2.4.0-p1/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/kissplice-2.4.0-p1/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-2.4.0-p1 -B/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -1569,49 +1603,49 @@ make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/CMakeFiles/ks_error_removal.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/CMakeFiles/ks_print_bcc.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +make -f debruijn-v4/CMakeFiles/ks_debruijn4.dir/build.make debruijn-v4/CMakeFiles/ks_debruijn4.dir/build [ 6%] Built target ks_error_removal [ 10%] Built target ks_print_bcc -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make -f debruijn-v4/CMakeFiles/ks_debruijn4.dir/build.make debruijn-v4/CMakeFiles/ks_debruijn4.dir/build make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/CMakeFiles/ks_clean_duplicates.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build'. -make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 22%] Built target ks_clean_duplicates -make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/CMakeFiles/ks_bubble_enumeration.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/CMakeFiles/ks_run_modules.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build'. +make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[ 37%] Built target ks_kissreadsSplice -[ 50%] Built target ks_bubble_enumeration -[ 65%] Built target ks_kissreadsSNPS -[ 79%] Built target ks_run_modules make[3]: Entering directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'debruijn-v4/CMakeFiles/ks_debruijn4.dir/build'. make[3]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' -[100%] Built target ks_debruijn4 +[ 22%] Built target ks_clean_duplicates +[ 37%] Built target ks_kissreadsSplice +[ 58%] Built target ks_debruijn4 +[ 70%] Built target ks_bubble_enumeration +[ 84%] Built target ks_run_modules +[100%] Built target ks_kissreadsSNPS make[2]: Leaving directory '/build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.4.0-p1/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall @@ -1659,20 +1693,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'kissplice' in '../kissplice_2.4.0-p1-4_amd64.deb'. dpkg-deb: building package 'kissplice-dbgsym' in '../kissplice-dbgsym_2.4.0-p1-4_amd64.deb'. +dpkg-deb: building package 'kissplice' in '../kissplice_2.4.0-p1-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../kissplice_2.4.0-p1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/55932/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/55932/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/16685 and its subdirectories -I: Current time: Mon Jan 10 12:55:32 -12 2022 -I: pbuilder-time-stamp: 1641862532 +I: removing directory /srv/workspace/pbuilder/55932 and its subdirectories +I: Current time: Wed Dec 9 08:35:01 +14 2020 +I: pbuilder-time-stamp: 1607452501