Diff of the two buildlogs: -- --- b1/build.log 2024-07-05 10:31:55.933525480 +0000 +++ b2/build.log 2024-07-05 10:35:34.768228890 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 4 22:24:53 -12 2024 -I: pbuilder-time-stamp: 1720175093 +I: Current time: Fri Aug 8 06:54:56 +14 2025 +I: pbuilder-time-stamp: 1754585696 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./mothur_1.44.3-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.N05O3UQ7/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 4 18:19:26 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.4UYjDeJn/trustedkeys.kbx': General error +gpgv: Signature made Sat Dec 5 20:19:26 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,166 @@ dpkg-source: info: applying drop_sys_sysctl.h.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/15092/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 8 06:55 /bin/sh -> /bin/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/142481/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=42 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0c03d0ca763a443fa2318ae249c955e3' - 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='15092' - PS1='# ' - PS2='> ' + INVOCATION_ID=0b68ff0a26a24c52a1646b99ff9b256f + 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=142481 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/r-b-build.XHTNxxHT/pbuilderrc_xzsM --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XHTNxxHT/b1 --logfile b1/build.log mothur_1.44.3-2.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://46.16.76.132:3128' + 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/r-b-build.XHTNxxHT/pbuilderrc_rm9U --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XHTNxxHT/b2 --logfile b2/build.log mothur_1.44.3-2.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://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 22:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 22:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 22:09 more - -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount - -rwxr-xr-x 1 root root 18664 Mar 27 22:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 22:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 21:59 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 22:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 22:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/15092/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 2024 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 2024 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 2024 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 2024 more + -rwsr-xr-x 1 root root 55528 Mar 29 2024 mount + -rwxr-xr-x 1 root root 18664 Mar 29 2024 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Aug 8 06:55 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 2024 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 2024 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 2024 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -251,7 +282,7 @@ Get: 46 http://deb.debian.org/debian bullseye/main amd64 libncurses-dev amd64 6.2+20201114-2+deb11u2 [344 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libreadline-dev amd64 8.1-1 [148 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 51.0 MB in 4s (13.3 MB/s) +Fetched 51.0 MB in 0s (121 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -461,7 +492,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mothur-1.44.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mothur_1.44.3-2_source.changes +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mothur-1.44.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mothur_1.44.3-2_source.changes dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.44.3-2 dpkg-buildpackage: info: source distribution unstable @@ -487,7 +522,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/mothur-1.44.3' dh_auto_build -- 64BIT_VERSION=yes - make -j20 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes + make -j42 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes make[2]: Entering directory '/build/reproducible-path/mothur-1.44.3' g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp @@ -538,6 +573,8 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::string, std::vector >&, std::vector >)': source/utils.cpp:771:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 771 | system(versionTestCommand.c_str()); @@ -554,8 +591,6 @@ source/utils.cpp:2054:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2054 | system("clear"); | ~~~~~~^~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp @@ -686,6 +721,13 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.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] + 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp In file included from /usr/include/string.h:495, from source/clearcut/distclearcut.cpp:54: In function 'char* strncpy(char*, const char*, size_t)', @@ -697,13 +739,6 @@ source/clearcut/distclearcut.cpp:155:12: note: length computed here 155 | strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.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] - 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp @@ -718,19 +753,36 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:607:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': source/commands/chimeravsearchcommand.cpp:480:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 480 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp +source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': +source/commands/clustercommand.cpp:557:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 557 | system(commandString.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp In file included from /usr/include/string.h:495, from source/mothur.h:45, from source/commands/command.hpp:16, @@ -745,9 +797,6 @@ source/commands/chimerauchimecommand.cpp:577:39: note: at offset 0 to an object with size 5 allocated by 'operator new []' here 577 | char* tempucl = new char[5]; | ^ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp In file included from /usr/include/string.h:495, from source/mothur.h:45, from source/commands/command.hpp:16, @@ -758,8 +807,12 @@ /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=] 90 | return __builtin___strcpy_chk (__dest, __src, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp +source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)': +source/commands/clustersplitcommand.cpp:1188:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1188 | system(commandString.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp In file included from /usr/include/string.h:495, from source/mothur.h:45, from source/commands/command.hpp:16, @@ -770,41 +823,19 @@ /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=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp -source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': -source/commands/clustercommand.cpp:557:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 557 | system(commandString.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp -source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)': -source/commands/clustersplitcommand.cpp:1188:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1188 | system(commandString.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp -source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': -source/commands/distancecommand.cpp:332:10: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 332 | system(("gzip -v " + outputFile).c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.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 - 77 | vector Venn::getPic(vector lookup, vector vCalcs, vector thisOtuLabels) { - | ^~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp +source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': +source/commands/distancecommand.cpp:332:10: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 332 | system(("gzip -v " + outputFile).c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp @@ -836,16 +867,16 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp -source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)': -source/commands/makefilecommand.cpp:353:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 353 | system(findCommand.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp +source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)': +source/commands/makefilecommand.cpp:353:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 353 | system(findCommand.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergeotuscommand.o source/commands/mergeotuscommand.cpp @@ -864,11 +895,11 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:268:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp @@ -910,15 +941,19 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp -source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()': -source/commands/systemcommand.cpp:99:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | system(command.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.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 + 77 | vector Venn::getPic(vector lookup, vector vCalcs, vector thisOtuLabels) { + | ^~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp +source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()': +source/commands/systemcommand.cpp:99:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | system(command.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp @@ -928,15 +963,17 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string, bool)': source/datastructures/blastalign.cpp:65:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp source/datastructures/blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestSequences(Sequence*, int, std::vector&) const': source/datastructures/blastdb.cpp:164:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 164 | system(blastCommand.c_str()); @@ -949,8 +986,6 @@ source/datastructures/blastdb.cpp:294:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 294 | system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -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 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/mothur-1.44.3=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.3\"" -DUSE_READLINE -Isource -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/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp @@ -1088,12 +1123,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/142481/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/142481/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/15092 and its subdirectories -I: Current time: Thu Jul 4 22:31:55 -12 2024 -I: pbuilder-time-stamp: 1720175515 +I: removing directory /srv/workspace/pbuilder/142481 and its subdirectories +I: Current time: Fri Aug 8 06:58:31 +14 2025 +I: pbuilder-time-stamp: 1754585911