Diff of the two buildlogs: -- --- b1/build.log 2021-12-30 23:12:54.089727875 +0000 +++ b2/build.log 2021-12-30 23:17:04.977918098 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 1 17:21:49 -12 2023 -I: pbuilder-time-stamp: 1675315309 +I: Current time: Fri Dec 31 13:12:56 +14 2021 +I: pbuilder-time-stamp: 1640905976 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./plast_2.3.2+dfsg-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.L6LZr9tc/trustedkeys.kbx': General error -gpgv: Signature made Sat Jan 30 22:25:45 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.fg3L_0Lr/trustedkeys.kbx': General error +gpgv: Signature made Mon Feb 1 00:25:45 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plast_2.3.2+dfsg-7.dsc @@ -32,135 +32,169 @@ dpkg-source: info: applying simde.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1928170/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1425621/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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/1425621/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1425621/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,-fixfilepath 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath 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='c89479e9995646758c62fc479b77b368' - 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='1928170' - PS1='# ' - PS2='> ' + INVOCATION_ID=d0407de45bce4e31b0bc8fa2fb39b357 + 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=1425621 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.ij5K0lKzm0/pbuilderrc_fNKF --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ij5K0lKzm0/b1 --logfile b1/build.log plast_2.3.2+dfsg-7.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.ij5K0lKzm0/pbuilderrc_Qt8d --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ij5K0lKzm0/b2 --logfile b2/build.log plast_2.3.2+dfsg-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1928170/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 31 13:13 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1425621/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -336,7 +370,7 @@ Get: 130 http://deb.debian.org/debian bullseye/main amd64 libpcrecpp0v5 amd64 2:8.39-13 [152 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libpcre3-dev amd64 2:8.39-13 [650 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libsimde-dev all 0.7.2-4 [259 kB] -Fetched 340 MB in 22s (15.5 MB/s) +Fetched 340 MB in 6s (54.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -1058,7 +1092,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/plast-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plast_2.3.2+dfsg-7_source.changes +hostname: Name or service not known +I: Running cd /build/plast-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plast_2.3.2+dfsg-7_source.changes dpkg-buildpackage: info: source package plast dpkg-buildpackage: info: source version 2.3.2+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -1141,7 +1176,7 @@ set -e ; for SIMD in sse3 ; do \ dh_auto_build --builddirectory=obj-${SIMD} ; \ done - cd obj-sse3 && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-sse3 && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/plast-2.3.2+dfsg/obj-sse3' /usr/bin/cmake -S/build/plast-2.3.2+dfsg -B/build/plast-2.3.2+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles /build/plast-2.3.2+dfsg/obj-sse3//CMakeFiles/progress.marks @@ -1153,266 +1188,349 @@ cd /build/plast-2.3.2+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/plast-2.3.2+dfsg /build/plast-2.3.2+dfsg /build/plast-2.3.2+dfsg/obj-sse3 /build/plast-2.3.2+dfsg/obj-sse3 /build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/plast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/plast-2.3.2+dfsg/obj-sse3' cd /build/plast-2.3.2+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/plast-2.3.2+dfsg /build/plast-2.3.2+dfsg /build/plast-2.3.2+dfsg/obj-sse3 /build/plast-2.3.2+dfsg/obj-sse3 /build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/DependInfo.cmake --color= -Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/DependInfo.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/depend.internal". -Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/depend.internal". Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/plast.dir/DependInfo.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/plast.dir/depend.internal". Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/plast.dir/depend.internal". -Scanning dependencies of target PlastLibrary -make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-sse3' -make -f CMakeFiles/PlastLibrary.dir/build.make CMakeFiles/PlastLibrary.dir/build +Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/DependInfo.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/depend.internal". +Dependee "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/plast-2.3.2+dfsg/obj-sse3/CMakeFiles/PlastLibrary.dir/depend.internal". Scanning dependencies of target plast make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-sse3' make -f CMakeFiles/plast.dir/build.make CMakeFiles/plast.dir/build +Scanning dependencies of target PlastLibrary +make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-sse3' +make -f CMakeFiles/PlastLibrary.dir/build.make CMakeFiles/PlastLibrary.dir/build make[4]: Entering directory '/build/plast-2.3.2+dfsg/obj-sse3' -[ 0%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o make[4]: Entering directory '/build/plast-2.3.2+dfsg/obj-sse3' -[ 0%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o +[ 0%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AbstractAlgorithm.cpp +[ 0%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o +[ 0%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o +[ 1%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AbstractAlgorithm.cpp -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AlgoIndexatorNucleotide.cpp -[ 1%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o -[ 1%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/BasicAlgoIndexator.cpp -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AlgorithmPlastn.cpp -[ 1%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DatabasesProvider.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DatabasesProvider.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/DatabasesProvider.cpp -[ 1%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o -[ 2%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DefaultAlgoConfig.cpp.o -[ 2%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o +[ 1%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AlgoIndexatorNucleotide.cpp -[ 3%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AbstractAlgorithm.cpp -[ 3%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/DefaultAlgoConfig.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoConfig.cpp /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o +[ 2%] Building CXX object CMakeFiles/PlastLibrary.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o +[ 2%] Building CXX object CMakeFiles/plast.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o -c /build/plast-2.3.2+dfsg/src/algo/core/impl/AlgorithmPlastn.cpp +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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Building CXX object CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp +[ 44%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp -[ 37%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o +[ 44%] Building CXX object CMakeFiles/plast.dir/src/database/impl/CompositeSequenceDatabase.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/CompositeSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/CompositeSequenceDatabase.cpp +[ 45%] Building CXX object CMakeFiles/plast.dir/src/database/impl/DefaultAlphabet.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/DefaultAlphabet.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/DefaultAlphabet.cpp +[ 46%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp -[ 37%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbFileIndexReader.cpp.o +[ 46%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbFileIndexReader.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbFileIndexReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.cpp -[ 37%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbSequenceIterator.cpp.o +[ 46%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbSequenceIterator.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp -[ 37%] Building CXX object CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentSplitterBanded.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentSplitterBanded.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitterBanded.cpp -[ 38%] Building CXX object CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlign.cpp.o -[ 39%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlign.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlign.cpp +[ 47%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BufferedCachedSequenceDatabase.cpp -[ 39%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedSequenceDatabase.cpp.o +[ 47%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedSequenceDatabase.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/BufferedSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp -[ 39%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/CompositeSequenceDatabase.cpp.o +[ 47%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaSequenceIterator.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaSequenceOutput.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaSequenceOutput.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp +[ 49%] Building CXX object CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In member function 'virtual int database::impl::FastaDatabaseQuickReader::load(const string&)': +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:200:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 200 | fread (&magic, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:211:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 211 | fread (&len, sizeof(size_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:215:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | fread (buffer, sizeof(char), len, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:231:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | fread (&_totalSize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:234:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | fread (&_dataSize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:237:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fread (&_nbSequences, sizeof(u_int32_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:240:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 240 | fread (&_dbKind, sizeof(DatabaseKind_e), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:243:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 243 | fread (&_maxblocksize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:247:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 247 | fread (&nbOffsets, sizeof(size_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:253:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 253 | fread (&offset, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In static member function 'static bool database::impl::FastaDatabaseQuickReader::isQuickReaderFile(const string&)': +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:373:37: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 373 | u_int64_t magic = 0; fread (&magic, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 49%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/CompositeSequenceDatabase.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/CompositeSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/CompositeSequenceDatabase.cpp -[ 39%] Building CXX object CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlignTraceback.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlignTraceback.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlignTraceback.cpp -[ 39%] Building CXX object CMakeFiles/plast.dir/src/alignment/visitors/impl/CompareContainerVisitor.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops 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CMakeFiles/plast.dir/src/alignment/visitors/impl/CompareResultVisitor.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/visitors/impl/CompareResultVisitor.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareResultVisitor.cpp -[ 41%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o +[ 50%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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CXX object CMakeFiles/plast.dir/src/alignment/visitors/impl/QueryReorderVisitor.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/visitors/impl/QueryReorderVisitor.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In member function 'virtual int database::impl::FastaDatabaseQuickReader::load(const string&)': /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:200:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | fread (&magic, sizeof(u_int64_t), 1, file); @@ -1448,188 +1566,174 @@ /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:373:37: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 373 | u_int64_t magic = 0; fread (&magic, sizeof(u_int64_t), 1, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object CMakeFiles/plast.dir/src/alignment/visitors/impl/ReverseStrandVisitor.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/alignment/visitors/impl/ReverseStrandVisitor.cpp.o -c 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+/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp: In destructor 'dp::impl::SystemCommand::~SystemCommand()': +/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 119 | system (tmp); + | ~~~~~~~^~~~~ +[ 58%] Building CXX object CMakeFiles/plast.dir/src/index/impl/DatabaseIndex.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/index/impl/DatabaseIndex.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp +[ 59%] Building CXX object 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-D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/designpattern/impl/XmlReader.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/XmlReader.cpp -[ 52%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BasicSequenceBuilder.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BasicSequenceBuilder.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp: In destructor 'dp::impl::SystemCommand::~SystemCommand()': -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 119 | system (tmp); - | ~~~~~~~^~~~~ -[ 52%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/AbstractDatabaseIndex.cpp.o +[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/AbstractDatabaseIndex.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/AbstractDatabaseIndex.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/AbstractDatabaseIndex.cpp -[ 52%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp -[ 52%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndex.cpp.o +[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndex.cpp.o +[ 64%] Building C object CMakeFiles/plast.dir/src/index/impl/retrievall.c.o +/usr/bin/cc -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include 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CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndexHash.cpp.o +/build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static + 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); + | ^~~~~~~~~~~~~~ +[ 64%] Building CXX object CMakeFiles/plast.dir/src/launcher/core/PlastCmd.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/core/PlastCmd.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.cpp +[ 65%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndexHash.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndexHash.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseIndexHash.cpp -[ 53%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o +[ 65%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndex.cpp -[ 53%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndexOptim.cpp.o +/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp: In destructor 'dp::impl::SystemCommand::~SystemCommand()': +/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 119 | system (tmp); + | ~~~~~~~^~~~~ +[ 65%] Building CXX object CMakeFiles/plast.dir/src/launcher/core/PlastOptionsParser.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include 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CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndexOptim.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndexOptim.cpp -[ 54%] Building C object CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o +[ 66%] Building C object CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o /usr/bin/cc -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o -c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); | ^~~~~~~~~~~~~~ -[ 55%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp -[ 55%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/core/PlastCmd.cpp.o +[ 67%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/Helper.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include 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/build/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.cpp -[ 55%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.cpp -[ 55%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/core/PlastOptionsParser.cpp.o +[ 67%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/core/PlastOptionsParser.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include 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-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/CompositeSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/CompositeSequenceDatabase.cpp -[ 58%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.cpp.o +[ 70%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.cpp -[ 58%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp.o +[ 70%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp -[ 59%] Building CXX object CMakeFiles/plast.dir/src/database/impl/DefaultAlphabet.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/DefaultAlphabet.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/DefaultAlphabet.cpp -[ 59%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp -[ 59%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o +[ 70%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp +[ 71%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp +[ 71%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp -[ 60%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o +[ 71%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp +[ 71%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp +[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp -[ 61%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaSequenceIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp -[ 61%] Building CXX object CMakeFiles/plast.dir/src/database/impl/FastaSequenceOutput.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/FastaSequenceOutput.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp -[ 61%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o +[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp -[ 61%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o +[ 73%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.cpp +[ 73%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoExecutionObserver.cpp +[ 73%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp -[ 62%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o +[ 74%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.cpp -[ 62%] Building CXX object CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In member function 'virtual int database::impl::FastaDatabaseQuickReader::load(const string&)': -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:200:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 200 | fread (&magic, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:211:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 211 | fread (&len, sizeof(size_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:215:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | fread (buffer, sizeof(char), len, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:231:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | fread (&_totalSize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:234:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | fread (&_dataSize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:237:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fread (&_nbSequences, sizeof(u_int32_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:240:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 240 | fread (&_dbKind, sizeof(DatabaseKind_e), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:243:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 243 | fread (&_maxblocksize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:247:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 247 | fread (&nbOffsets, sizeof(size_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:253:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 253 | fread (&offset, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In static member function 'static bool database::impl::FastaDatabaseQuickReader::isQuickReaderFile(const string&)': -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:373:37: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 373 | u_int64_t magic = 0; fread (&magic, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o +[ 74%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoExecutionObserver.cpp -[ 62%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o +/build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp: In function 'jlong Java_org_inria_genscale_dbscan_impl_plast_RequestManager_createPeerRequest(JNIEnv*, jobject, jobject)': +/build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:316:1: warning: control reaches end of non-void function [-Wreturn-type] + 316 | } + | ^ +[ 74%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp +[ 74%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp -[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoResultObserver.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp +[ 75%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp +[ 75%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/BargraphObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/BargraphObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp: In function 'jlong Java_org_inria_genscale_dbscan_impl_plast_RequestManager_createPeerRequest(JNIEnv*, jobject, jobject)': /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:316:1: warning: control reaches end of non-void function [-Wreturn-type] 316 | } | ^ -[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/BargraphObserver.cpp.o +[ 76%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoResultObserver.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp +[ 76%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/FileProgressionObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include 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CMakeFiles/PlastLibrary.dir/src/launcher/observers/BargraphObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp -[ 64%] Building CXX object CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp -[ 64%] Building CXX object CMakeFiles/plast.dir/src/database/impl/ReverseStrandSequenceIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include 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-[ 65%] Building CXX object CMakeFiles/plast.dir/src/database/impl/SequenceTokenizer.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/SequenceTokenizer.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/SequenceTokenizer.cpp -[ 65%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/FileProgressionObserver.cpp.o +[ 77%] Building CXX object CMakeFiles/plast.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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/build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp -[ 65%] Building CXX object CMakeFiles/plast.dir/src/database/impl/StringSequenceIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/StringSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp -[ 65%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/CommandDispatcher.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. 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/build/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp +[ 78%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.cpp -[ 66%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/ObsfucatedString.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/ObsfucatedString.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp -[ 67%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/OptionsParser.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/OptionsParser.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp -[ 68%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/ConfigFileProperties.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/designpattern/impl/ConfigFileProperties.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/ConfigFileProperties.cpp -[ 68%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/DirectoryIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/designpattern/impl/DirectoryIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/DirectoryIterator.cpp /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp: In member function 'virtual void launcher::observers::ResourcesObserver::update(dp::EventInfo*, dp::ISubject*)': /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp:256:44: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] 256 | fprintf (_file, "%ld %.3f %lld %lld %.3f %.3f %.3f %d %lld %lld \n", @@ -1675,146 +1779,18 @@ | ~~~~~~~~~~~~~~~~ | | | u_int64_t {aka long unsigned int} -[ 68%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/FileLineIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include 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/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp -[ 71%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemory.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp -[ 71%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/TokenizerIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/designpattern/impl/TokenizerIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/TokenizerIterator.cpp -[ 71%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemoryFile.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp -[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxThread.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp -/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp: In destructor 'os::impl::LinuxFile::~LinuxFile()': -/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 42 | system (ss.str().c_str()); - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object CMakeFiles/plast.dir/src/designpattern/impl/WrapperIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/designpattern/impl/WrapperIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/WrapperIterator.cpp -[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxTime.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxTime.cpp -[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsFile.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsFile.cpp -/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp: In member function 'virtual u_int32_t os::impl::LinuxMemoryAllocator::getMemUsage()': -/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:46:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 46 | fgets (buffer, sizeof(buffer), file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp: In destructor 'dp::impl::SystemCommand::~SystemCommand()': -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 119 | system (tmp); - | ~~~~~~~^~~~~ -[ 73%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemory.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o 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-I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/seed/impl/AbstractSeedIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/seed/impl/AbstractSeedIterator.cpp -[ 79%] Building CXX object CMakeFiles/PlastLibrary.dir/src/seed/impl/BasicSeedModel.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/seed/impl/BasicSeedModel.cpp.o -c /build/plast-2.3.2+dfsg/src/seed/impl/BasicSeedModel.cpp -[ 79%] Building CXX object CMakeFiles/PlastLibrary.dir/src/seed/impl/SubSeedModel.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/seed/impl/SubSeedModel.cpp.o -c /build/plast-2.3.2+dfsg/src/seed/impl/SubSeedModel.cpp -[ 79%] Building CXX object CMakeFiles/plast.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat 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CMakeFiles/PlastLibrary.dir/src/seg/impl/genwin.c.o -c /build/plast-2.3.2+dfsg/src/seg/impl/genwin.c -[ 81%] Building C object CMakeFiles/PlastLibrary.dir/src/seg/impl/seg.c.o -/usr/bin/cc -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/seg/impl/seg.c.o -c /build/plast-2.3.2+dfsg/src/seg/impl/seg.c -[ 81%] Building CXX object CMakeFiles/plast.dir/src/index/impl/DatabaseNucleotidIndexOptim.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong 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/build/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.cpp -/build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static - 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); - | ^~~~~~~~~~~~~~ -[ 82%] Building CXX object CMakeFiles/plast.dir/src/launcher/core/PlastOptionsParser.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/core/PlastOptionsParser.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/core/PlastOptionsParser.cpp -[ 83%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/Helper.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/Helper.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/Helper.cpp -[ 83%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/Wrapper.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o 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CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp -[ 85%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp -[ 85%] Building CXX object 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CMakeFiles/plast.dir/src/os/impl/LinuxFile.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp: In member function 'virtual void launcher::observers::ResourcesObserver::update(dp::EventInfo*, dp::ISubject*)': /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp:256:44: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'u_int64_t' {aka 'long unsigned int'} [-Wformat=] 256 | fprintf (_file, "%ld %.3f %lld %lld %.3f %.3f %.3f %d %lld %lld \n", @@ -1860,80 +1836,139 @@ | ~~~~~~~~~~~~~~~~ | | | u_int64_t {aka long unsigned int} -[ 90%] Building CXX object CMakeFiles/plast.dir/src/misc/impl/RangeTree.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/misc/impl/RangeTree.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/RangeTree.cpp -[ 90%] Building CXX object CMakeFiles/plast.dir/src/os/impl/DefaultOsFactory.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/DefaultOsFactory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/DefaultOsFactory.cpp -[ 91%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxFile.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp -[ 91%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o +[ 81%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/RangeTree.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/RangeTree.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/RangeTree.cpp +[ 81%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/DefaultOsFactory.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/DefaultOsFactory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/DefaultOsFactory.cpp +[ 82%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxFile.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp +[ 82%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp -[ 91%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o +[ 82%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp -[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o +[ 83%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp -make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-sse3' -[ 92%] Built target PlastLibrary -[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o +/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp: In destructor 'os::impl::LinuxFile::~LinuxFile()': +/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 42 | system (ss.str().c_str()); + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 83%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxTime.cpp -[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsFile.cpp -[ 93%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.cpp -[ 93%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.cpp -[ 93%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp +[ 83%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemory.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp +[ 83%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemoryFile.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp +[ 84%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxThread.cpp.o /build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp: In destructor 'os::impl::LinuxFile::~LinuxFile()': /build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 42 | system (ss.str().c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 94%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp +[ 84%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxTime.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxTime.cpp +[ 84%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsFile.cpp +[ 84%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsFile.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsFile.cpp +[ 85%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemory.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.cpp +[ 86%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.cpp +[ 86%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemoryFile.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.cpp +/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp: In member function 'virtual u_int32_t os::impl::LinuxMemoryAllocator::getMemUsage()': +/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:46:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 46 | fgets (buffer, sizeof(buffer), file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-sse3/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.cpp +[ 86%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsThread.cpp.o +/usr/bin/c++ 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CMakeFiles/plast.dir/src/database/impl/BasicSequenceBuilder.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp -[ 34%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o +[ 45%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp -[ 34%] Building CXX object CMakeFiles/PlastLibrary.dir/src/alignment/filter/impl/AlignmentFilterFactory.cpp.o -/usr/bin/c++ 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-Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp -[ 35%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o +[ 46%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp +[ 46%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.cpp -[ 35%] Building CXX object CMakeFiles/PlastLibrary.dir/src/alignment/filter/impl/AlignmentFilterOperator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/alignment/filter/impl/AlignmentFilterOperator.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterOperator.cpp -[ 35%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbSequenceIterator.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp -[ 36%] Building CXX object CMakeFiles/PlastLibrary.dir/src/alignment/filter/impl/AlignmentFilterXML.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/alignment/filter/impl/AlignmentFilterXML.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.cpp -[ 36%] Building CXX object CMakeFiles/PlastLibrary.dir/src/alignment/tools/impl/AlignmentContainerShrinkCmd.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include 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-D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/FastaSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BufferedCachedSequenceDatabase.cpp -[ 38%] Building CXX object CMakeFiles/PlastLibrary.dir/src/alignment/tools/impl/AlignmentOverlapCmd.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/alignment/tools/impl/AlignmentOverlapCmd.cpp.o -c /build/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentOverlapCmd.cpp -[ 38%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BlastdbSequenceIterator.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BlastdbSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp +[ 48%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/FastaSequenceOutput.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/FastaSequenceOutput.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In member function 'virtual int database::impl::FastaDatabaseQuickReader::load(const string&)': +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:200:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 200 | fread (&magic, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:211:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 211 | fread (&len, sizeof(size_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:215:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | fread (buffer, sizeof(char), len, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:231:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 231 | fread (&_totalSize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:234:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | fread (&_dataSize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:237:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fread (&_nbSequences, sizeof(u_int32_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:240:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 240 | fread (&_dbKind, sizeof(DatabaseKind_e), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:243:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 243 | fread (&_maxblocksize, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:247:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 247 | fread (&nbOffsets, sizeof(size_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:253:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 253 | fread (&offset, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In static member function 'static bool database::impl::FastaDatabaseQuickReader::isQuickReaderFile(const string&)': +/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:373:37: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 373 | u_int64_t magic = 0; fread (&magic, sizeof(u_int64_t), 1, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp +[ 48%] Building CXX object CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp -[ 38%] Building CXX object CMakeFiles/plast.dir/src/database/impl/CompositeSequenceDatabase.cpp.o +[ 49%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -c 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CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp +[ 55%] Building CXX object CMakeFiles/PlastLibrary.dir/src/designpattern/impl/TokenizerIterator.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat 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+/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 119 | system (tmp); + | ~~~~~~~^~~~~ +[ 56%] Building CXX object CMakeFiles/PlastLibrary.dir/src/designpattern/impl/WrapperIterator.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/designpattern/impl/WrapperIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/WrapperIterator.cpp +[ 57%] Building CXX object CMakeFiles/PlastLibrary.dir/src/designpattern/impl/XmlReader.cpp.o 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CMakeFiles/plast.dir/src/designpattern/impl/CommandDispatcher.cpp.o +[ 60%] Building C object CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o +/usr/bin/cc -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o -c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c +/build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static + 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); + | ^~~~~~~~~~~~~~ +[ 60%] Building CXX object 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CMakeFiles/plast.dir/src/index/impl/retrievall.c.o /usr/bin/cc -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/index/impl/retrievall.c.o -c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); | ^~~~~~~~~~~~~~ -[ 55%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ 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object CMakeFiles/plast.dir/src/launcher/jni/Helper.cpp.o +[ 70%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp +[ 73%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/AlgoResultObserver.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. 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/build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp -[ 60%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/FastaSequenceOutput.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/FastaSequenceOutput.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp -[ 61%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o +[ 74%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp -[ 61%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp -[ 61%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o +[ 74%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In member function 'virtual int database::impl::FastaDatabaseQuickReader::load(const string&)': -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:200:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 200 | fread (&magic, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:211:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 211 | fread (&len, sizeof(size_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:215:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | fread (buffer, sizeof(char), len, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:231:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 231 | fread (&_totalSize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:234:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | fread (&_dataSize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:237:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fread (&_nbSequences, sizeof(u_int32_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:240:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 240 | fread (&_dbKind, sizeof(DatabaseKind_e), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:243:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 243 | fread (&_maxblocksize, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:247:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 247 | fread (&nbOffsets, sizeof(size_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:253:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 253 | fread (&offset, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp: In static member function 'static bool database::impl::FastaDatabaseQuickReader::isQuickReaderFile(const string&)': -/build/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:373:37: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 373 | u_int64_t magic = 0; fread (&magic, sizeof(u_int64_t), 1, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o +[ 74%] Building CXX object CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp -[ 62%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o +[ 75%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.cpp -[ 62%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o +[ 75%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/BargraphObserver.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/BargraphObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp +[ 75%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoExecutionObserver.cpp -[ 62%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp -[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp -[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/ReverseStrandSequenceIterator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/ReverseStrandSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/ReverseStrandSequenceIterator.cpp -[ 63%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/Sequence.cpp.o -[ 64%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/Sequence.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/Sequence.cpp -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp -[ 65%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/SequenceTokenizer.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/SequenceTokenizer.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/SequenceTokenizer.cpp +[ 75%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/observers/FileProgressionObserver.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/observers/FileProgressionObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp +[ 76%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.cpp /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp: In function 'jlong Java_org_inria_genscale_dbscan_impl_plast_RequestManager_createPeerRequest(JNIEnv*, jobject, jobject)': /build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:316:1: warning: control reaches end of non-void function [-Wreturn-type] 316 | } | ^ -[ 65%] Building CXX object CMakeFiles/PlastLibrary.dir/src/database/impl/StringSequenceIterator.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/database/impl/StringSequenceIterator.cpp.o -c /build/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp -[ 65%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/BargraphObserver.cpp.o +[ 76%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/ObsfucatedString.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/ObsfucatedString.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp +[ 76%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp +[ 77%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp +[ 77%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/BargraphObserver.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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/build/plast-2.3.2+dfsg/src/designpattern/impl/CommandDispatcher.cpp -[ 65%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/FileProgressionObserver.cpp.o +[ 78%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/OptionsParser.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/OptionsParser.cpp.o -c /build/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp +[ 78%] Building CXX object CMakeFiles/plast.dir/src/launcher/observers/FileProgressionObserver.cpp.o /usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include 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CMakeFiles/PlastLibrary.dir/src/designpattern/impl/Property.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/designpattern/impl/Property.cpp.o -c /build/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp: In member function 'virtual void launcher::observers::ResourcesObserver::update(dp::EventInfo*, dp::ISubject*)': /build/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp:256:44: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'u_int64_t' {aka 'long unsigned 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-fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp -[ 72%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndex.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndex.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp: In destructor 'dp::impl::SystemCommand::~SystemCommand()': -/build/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:16: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 119 | system (tmp); - | ~~~~~~~^~~~~ -[ 72%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp -[ 73%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp -[ 74%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndexHash.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseIndexHash.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseIndexHash.cpp -[ 74%] Building CXX object CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o -c /build/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndex.cpp -/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp: In destructor 'os::impl::LinuxFile::~LinuxFile()': -/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 42 | system (ss.str().c_str()); - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxTime.cpp -[ 74%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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/build/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp -[ 76%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsTime.cpp +[ 81%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/LinuxMemoryFile.cpp.o +/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/index/impl/retrievall.c.o -c /build/plast-2.3.2+dfsg/src/index/impl/retrievall.c -/build/plast-2.3.2+dfsg/src/index/impl/retrievall.c:1075:9: warning: 'get_bits_value' is static but used in inline function 'get_packed_value' which is not static - 1075 | return get_bits_value(retr->packed_table,count,retr->vals_length,retr->bits_mask); - | ^~~~~~~~~~~~~~ -[ 81%] Building CXX object CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o -/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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CMakeFiles/PlastLibrary.dir/src/launcher/core/PlastOptionsParser.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/core/PlastOptionsParser.cpp -[ 82%] Building CXX object CMakeFiles/PlastLibrary.dir/src/launcher/jni/Helper.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/launcher/jni/Helper.cpp.o -c /build/plast-2.3.2+dfsg/src/launcher/jni/Helper.cpp -[ 83%] Building C object CMakeFiles/plast.dir/src/seg/impl/seg.c.o -/usr/bin/cc -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 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-/build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp: In function 'jlong Java_org_inria_genscale_dbscan_impl_plast_RequestManager_createPeerRequest(JNIEnv*, jobject, jobject)': -/build/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:316:1: warning: control reaches end of non-void function [-Wreturn-type] - 316 | } - | ^ -[ 90%] Building CXX object CMakeFiles/PlastLibrary.dir/src/misc/impl/RangeTree.cpp.o -/usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/misc/impl/RangeTree.cpp.o -c 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/build/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.cpp -make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' -[ 93%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsMemoryFile.cpp.o +/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp: In destructor 'os::impl::LinuxFile::~LinuxFile()': +/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 42 | system (ss.str().c_str()); + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 84%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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/build/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:20: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 42 | system (ss.str().c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 84%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsThread.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsThread.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp -/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp: In member function 'virtual u_int32_t os::impl::LinuxMemoryAllocator::getMemUsage()': -/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:46:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 46 | fgets (buffer, sizeof(buffer), file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 94%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsTime.cpp.o +[ 84%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp +[ 85%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsTime.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/PlastLibrary.dir/src/os/impl/MacOsTime.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/MacOsTime.cpp -[ 94%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/WindowsFile.cpp.o +[ 85%] Building CXX object CMakeFiles/PlastLibrary.dir/src/os/impl/WindowsFile.cpp.o /usr/bin/c++ -DPlastLibrary_EXPORTS -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. 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u_int32_t os::impl::LinuxMemoryAllocator::getMemUsage()': +/build/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:46:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 46 | fgets (buffer, sizeof(buffer), file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o +[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o +/usr/bin/c++ -D__LINUX__ -I/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -fdebug-prefix-map=/build/plast-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -fomit-frame-pointer -o CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o -c /build/plast-2.3.2+dfsg/src/os/impl/WindowsMemory.cpp 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CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o CMakeFiles/plast.dir/src/seg/impl/dust.c.o CMakeFiles/plast.dir/src/seg/impl/genwin.c.o CMakeFiles/plast.dir/src/seg/impl/seg.c.o CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o -o bin/None/plast -lpthread -lpcre make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' [100%] Built target PlastLibrary +make[4]: Leaving directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' +[100%] Built target plast make[3]: Leaving directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' @@ -2757,7 +2792,7 @@ I: Nothing to do for arch:indep binary make[1]: Leaving directory '/build/plast-2.3.2+dfsg' dh_auto_install -O--buildsystem=cmake -Nplast-example - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/plast-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/plast-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/plast-2.3.2+dfsg -B/build/plast-2.3.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -3066,8 +3101,8 @@ dh_gencontrol -O--buildsystem=cmake -Nplast dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'plast-dbgsym' in '../plast-dbgsym_2.3.2+dfsg-7_amd64.deb'. dpkg-deb: building package 'plast' in '../plast_2.3.2+dfsg-7_amd64.deb'. +dpkg-deb: building package 'plast-dbgsym' in '../plast-dbgsym_2.3.2+dfsg-7_amd64.deb'. dpkg-deb: building package 'plast-example' in '../plast-example_2.3.2+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../plast_2.3.2+dfsg-7_amd64.changes @@ -3076,12 +3111,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1425621/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1425621/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/1928170 and its subdirectories -I: Current time: Wed Feb 1 17:35:53 -12 2023 -I: pbuilder-time-stamp: 1675316153 +I: removing directory /srv/workspace/pbuilder/1425621 and its subdirectories +I: Current time: Fri Dec 31 13:17:04 +14 2021 +I: pbuilder-time-stamp: 1640906224