Diff of the two buildlogs: -- --- b1/build.log 2021-07-15 17:04:23.069491542 +0000 +++ b2/build.log 2021-07-15 17:17:25.192091643 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 17 11:20:19 -12 2022 -I: pbuilder-time-stamp: 1660778419 +I: Current time: Fri Jul 16 07:04:27 +14 2021 +I: pbuilder-time-stamp: 1626368667 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed Jan 30 00:06:33 2019 -12 +gpgv: Signature made Thu Jan 31 02:06:33 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,136 +29,170 @@ dpkg-source: info: applying 0001-Add-hardening-flags.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3338/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/55140/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/55140/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/55140/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1a5722741db84c1cbb4c612846158755' - 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='3338' - PS1='# ' - PS2='> ' + INVOCATION_ID=6f50dd7e6e274d3cb459e874f31c2c7d + 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=55140 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.B1kQKWo0UP/pbuilderrc_Tjmm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/b1 --logfile b1/build.log mothur_1.41.21-1.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.B1kQKWo0UP/pbuilderrc_CLyp --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/b2 --logfile b2/build.log mothur_1.41.21-1.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 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/3338/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 16 07:04 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/55140/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -289,7 +323,7 @@ Get: 83 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libreadline-dev amd64 7.0-5 [133 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 60.0 MB in 1s (79.7 MB/s) +Fetched 60.0 MB in 1s (70.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -658,7 +692,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/mothur-1.41.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/mothur-1.41.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.41.21-1 dpkg-buildpackage: info: source distribution unstable @@ -684,7 +718,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/mothur-1.41.21' dh_auto_build -- 64BIT_VERSION=yes - make -j16 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes + make -j15 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes make[2]: Entering directory '/build/mothur-1.41.21' g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp @@ -708,11 +742,11 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engine.o source/engine.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp source/mothur.cpp: In function 'int main(int, char**)': source/mothur.cpp:45:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system("clear"); ~~~~~~^~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp @@ -733,6 +767,7 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp source/utils.cpp: In member function 'int Utils::renameFile(std::__cxx11::string, std::__cxx11::string)': source/utils.cpp:873:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); @@ -745,7 +780,6 @@ source/utils.cpp:1576:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(makeDirectoryCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp @@ -865,11 +899,11 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%ld\n", &dmat->ntaxa); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp @@ -880,11 +914,11 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': source/commands/distancecommand.cpp:328:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("gzip -v " + outputFile).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp @@ -894,21 +928,21 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::__cxx11::string)': source/commands/makefilecommand.cpp:366:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(findCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp source/venn.cpp: In member function 'std::vector > Venn::getPic(std::vector, std::vector, std::vector >)': source/venn.cpp:77:16: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without vector Venn::getPic(vector lookup, vector vCalcs, vector thisOtuLabels) { ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp @@ -917,20 +951,20 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)': source/commands/clustercommand.cpp:637:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double, clusterData*)': source/commands/clustersplitcommand.cpp:1219:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp @@ -961,15 +995,17 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp source/commands/chimeravsearchcommand.cpp: In member function 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)': source/commands/chimeravsearchcommand.cpp:1191:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp In file included from /usr/include/string.h:494, from source/mothur.h:49, from source/commands/command.hpp:16, @@ -980,8 +1016,6 @@ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' writing 11 bytes into a region of size 9 overflows the destination [-Wstringop-overflow=] return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp @@ -1036,22 +1070,20 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:733:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:316:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("gzip -v " + outputFile).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp In file included from /usr/include/string.h:494, from source/mothur.h:49, from source/commands/command.hpp:16, @@ -1062,6 +1094,8 @@ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:90:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' writing 6 bytes into a region of size 5 overflows the destination [-Wstringop-overflow=] return __builtin___strcpy_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp @@ -1088,11 +1122,11 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)': source/datastructures/blastalign.cpp:64:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp @@ -1109,6 +1143,7 @@ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp +g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp source/datastructures/blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestSequences(Sequence*, int, std::vector&)': source/datastructures/blastdb.cpp:163:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blastCommand.c_str()); @@ -1121,7 +1156,6 @@ source/datastructures/blastdb.cpp:297:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp @@ -1398,7 +1432,7 @@ + cat tmp.stderr + rm -f tmp.stderr + ls -lh uchime --rwxr-xr-x 1 pbuilder1 pbuilder1 13M Aug 17 11:26 uchime +-rwxrwxr-x 1 pbuilder2 pbuilder2 13M Jul 16 07:12 uchime + sum uchime 21556 12450 g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/rarefact.o source/nast.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/collect.o source/seqnoise.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/vsearchfileparser.o source/noalign.o source/heatmapsim.o source/opticluster.o source/trialSwap2.o source/consensus.o source/nastreport.o source/fileoutput.o source/cluster.o source/refchimeratest.o source/wilcox.o source/needlemanoverlap.o source/utils.o source/sensspeccalc.o source/myseqdist.o source/subsample.o source/commandfactory.o source/heatmap.o source/weightedlinkage.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/mothur.o source/engine.o source/linearalgebra.o source/slibshuff.o source/optifitcluster.o source/dlibshuff.o source/currentfile.o source/summary.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/overlap.o source/calculators/unweighted.o source/calculators/sharedjabund.o source/calculators/chao1.o source/calculators/sharedjclass.o source/calculators/sharedsobscollectsummary.o source/calculators/gower.o source/calculators/tp.o source/calculators/prng.o source/calculators/ppv.o source/calculators/fpfn.o source/calculators/sharedjsd.o source/calculators/sharedthetan.o source/calculators/boneh.o source/calculators/uvest.o source/calculators/sharedkulczynskicody.o source/calculators/sharedsorabund.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/sharedochiai.o source/calculators/structchord.o source/calculators/accuracy.o source/calculators/fdr.o source/calculators/sharedkulczynski.o source/calculators/mcc.o source/calculators/sharedthetayc.o source/calculators/coverage.o source/calculators/sharedace.o source/calculators/sharedanderbergs.o source/calculators/sharedsobs.o source/calculators/fn.o source/calculators/parsimony.o source/calculators/sharedrjsd.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/spearman.o source/calculators/mempearson.o source/calculators/manhattan.o source/calculators/whittaker.o source/calculators/shannon.o source/calculators/sharedsorclass.o source/calculators/structeuclidean.o source/calculators/specificity.o source/calculators/sharedchao1.o source/calculators/qstat.o source/calculators/simpsoneven.o source/calculators/memchi2.o source/calculators/npshannon.o source/calculators/tn.o source/calculators/shannoneven.o source/calculators/bstick.o source/calculators/logsd.o source/calculators/solow.o source/calculators/fp.o source/calculators/sharedjest.o source/calculators/tptn.o source/calculators/odum.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedlennon.o source/calculators/structchi2.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/sharedkstest.o source/calculators/f1score.o source/calculators/sensitivity.o source/calculators/sharedmorisitahorn.o source/calculators/bergerparker.o source/calculators/npv.o source/calculators/canberra.o source/calculators/hamming.o source/calculators/shen.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/geom.o source/calculators/memeuclidean.o source/calculators/bootstrap.o source/calculators/jackknife.o source/calculators/weighted.o source/calculators/efron.o source/calculators/invsimpson.o source/calculators/sharedjackknife.o source/calculators/shannonrange.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/chimerarealigner.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/getopt_long.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/commands/clusterdoturcommand.o source/commands/distancecommand.o source/commands/mergetaxsummarycommand.o source/commands/quitcommand.o source/commands/matrixoutputcommand.o source/commands/subsamplecommand.o source/commands/removegroupscommand.o source/commands/indicatorcommand.o source/commands/chimerabellerophoncommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/getgroupscommand.o source/commands/kruskalwalliscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/classifyseqscommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/removedistscommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/createdatabasecommand.o source/commands/splitgroupscommand.o source/commands/treegroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/clustersplitcommand.o source/commands/seqerrorcommand.o source/commands/aligncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/heatmapcommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/parsefastaqcommand.o source/commands/rarefactcommand.o source/commands/mergeotuscommand.o source/commands/screenseqscommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/trimseqscommand.o source/commands/mgclustercommand.o source/commands/listseqscommand.o source/commands/makelefsecommand.o source/commands/sffmultiplecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/makecontigscommand.o source/commands/makelookupcommand.o source/commands/getcurrentcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/getcommandinfocommand.o source/commands/listotulabelscommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/removeotulabelscommand.o source/commands/chimeraperseuscommand.o source/commands/phylodiversitycommand.o source/commands/filtersharedcommand.o source/commands/anosimcommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/seqsummarycommand.o source/commands/pcacommand.o source/commands/makebiomcommand.o source/commands/metastatscommand.o source/commands/shhhercommand.o source/commands/sffinfocommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/cooccurrencecommand.o source/commands/preclustercommand.o source/commands/setdircommand.o source/commands/classifytreecommand.o source/commands/clusterfitcommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/sharedcommand.o source/commands/mergefilecommand.o source/commands/pcoacommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/getgroupcommand.o source/commands/makefastqcommand.o source/commands/helpcommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/deuniquetreecommand.o source/commands/binsequencecommand.o source/commands/getlistcountcommand.o source/commands/classifyotucommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/setseedcommand.o source/commands/homovacommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/chimeracheckcommand.o source/commands/getmimarkspackagecommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/rarefactsharedcommand.o source/commands/newcommandtemplate.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/commands/chopseqscommand.o source/commands/collectcommand.o source/commands/chimeraccodecommand.o source/commands/chimeraslayercommand.o source/commands/clearcutcommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/ordervector.o source/datastructures/optimatrix.o source/datastructures/fastamap.o source/datastructures/alignment.o source/datastructures/nameassignment.o source/datastructures/suffixtree.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/tree.o source/datastructures/kmeralign.o source/datastructures/blastalign.o source/datastructures/alignmentcell.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/rabundfloatvector.o source/datastructures/treenode.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sparsedistancematrix.o source/datastructures/oligos.o source/datastructures/counttable.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/designmap.o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedlistvector.o source/datastructures/sharedordervector.o source/datastructures/distancedb.o source/datastructures/sequenceparser.o source/datastructures/fastqread.o source/datastructures/kmer.o source/datastructures/optiblastmatrix.o source/datastructures/sparsematrix.o source/datastructures/fullmatrix.o source/datastructures/optirefmatrix.o source/datastructures/filefile.o source/datastructures/reportfile.o source/datastructures/listvector.o source/datastructures/sequencecountparser.o source/datastructures/treemap.o source/datastructures/alignmentdb.o source/datastructures/suffixdb.o source/datastructures/optidata.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/abstractdecisiontree.o source/randomforest/decisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/readblast.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readcolumn.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline @@ -1443,20 +1477,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'mothur' in '../mothur_1.41.21-1_amd64.deb'. dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.41.21-1_amd64.deb'. +dpkg-deb: building package 'mothur' in '../mothur_1.41.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mothur_1.41.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/55140/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/55140/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/3338 and its subdirectories -I: Current time: Wed Aug 17 11:27:23 -12 2022 -I: pbuilder-time-stamp: 1660778843 +I: removing directory /srv/workspace/pbuilder/55140 and its subdirectories +I: Current time: Fri Jul 16 07:17:23 +14 2021 +I: pbuilder-time-stamp: 1626369443