Thu Jul 15 16:57:17 UTC 2021 I: starting to build mothur/buster/amd64 on jenkins on '2021-07-15 16:57' Thu Jul 15 16:57:17 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/71791/console.log Thu Jul 15 16:57:17 UTC 2021 I: Downloading source for buster/mothur=1.41.21-1 --2021-07-15 16:57:17-- http://deb.debian.org/debian/pool/main/m/mothur/mothur_1.41.21-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2092 (2.0K) Saving to: ‘mothur_1.41.21-1.dsc’ 0K .. 100% 272M=0s 2021-07-15 16:57:17 (272 MB/s) - ‘mothur_1.41.21-1.dsc’ saved [2092/2092] Thu Jul 15 16:57:17 UTC 2021 I: mothur_1.41.21-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mothur Binary: mothur Architecture: any Version: 1.41.21-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Tomasz Buchert Homepage: http://www.mothur.org Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/mothur Vcs-Git: https://salsa.debian.org/med-team/mothur.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev Package-List: mothur deb science optional arch=any Checksums-Sha1: 4b291a77848c05842cf5eaaafff1bc62d02059ee 1627667 mothur_1.41.21.orig.tar.gz fb74a99a507cb2532f6af78baab528f1bfbb9b1c 20072 mothur_1.41.21-1.debian.tar.xz Checksums-Sha256: ef1a36c259335ca213acbdf6ce8909f2787c2a214a61acd727d24d0939b5ffde 1627667 mothur_1.41.21.orig.tar.gz 619d123897152718a5b3b151629275f80c86ea5fb66dbeb549faccf6e65f6777 20072 mothur_1.41.21-1.debian.tar.xz Files: 82ab0d0dde0caca72d0c0abdf2ef525f 1627667 mothur_1.41.21.orig.tar.gz f108d512e437f5907c75183caa4f4e06 20072 mothur_1.41.21-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxRk0kRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFWtQ//SePBbxJ7t7usqcpramJFTdmDwtjzrF6y Xf35qDDslyyrW0jH3AQcCAK55T4am8Fckq3Zb58Cl7pACBJttS6vjb6y64DBOccP /VHTkSdpGhUkakiuoLwbGRSEqfCvVIwPRQhAUV8tWWSCbDPXhPQ1QeVXKVm8Bnbd NfjlPh8cKKwKmMNDMcd18/IwLVugmWs5soUB9P8PsRlwADVz7zTQ7DYciWe4OwfG kor4f6/mhfNsTkv8Q8xwr984CW3i/+k+NZYQ1v/ipTSgmRRUQu9EGILSjXCmKCWG VYOxoZ2B2BeDQm3F62P27bI+RQ3HfjtvwYXf17oAfY/LoZq8gT1wGc7A8f53Yn6u fD9bHPISWLr/DOpvi1ov76vFxg7UuIEveTBTq2pGV2Evp5+LweiAdHtO5QhR2Q2h 8jfNnNaIn+BRbmqo82LbFsiWj+bhkV9vtYCDZ0z6/4mu9n/r8DgQ/cFZIiCaTUTz c0grnF65kV4CFlvI4tnaiGjxfMVYJfKc0JtGIchh2S/T0GRnurNP70qllh1IX8Tf tPHWuxScYGyMrBUHMo39SPDFjojBfh0EGc4wPJvygCC0dxtnq7snBz56aIPrDBgl MNrSMuSoB2CgbRtBzG+slV0JzxGGsSu4fgh3yi1M8pSyfJmpZhPvhNj5QVvl+lZ8 7+yy89wnn74= =bbgD -----END PGP SIGNATURE----- Thu Jul 15 16:57:17 UTC 2021 I: Checking whether the package is not for us Thu Jul 15 16:57:17 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Jul 15 16:57:17 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Jul 15 17:04:25 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 17 11:20:19 -12 2022 I: pbuilder-time-stamp: 1660778419 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mothur_1.41.21-1.dsc] I: copying [./mothur_1.41.21.orig.tar.gz] I: copying [./mothur_1.41.21-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 30 00:06:33 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mothur_1.41.21-1.dsc dpkg-source: info: extracting mothur in mothur-1.41.21 dpkg-source: info: unpacking mothur_1.41.21.orig.tar.gz dpkg-source: info: unpacking mothur_1.41.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Add-hardening-flags.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3338/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1a5722741db84c1cbb4c612846158755' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3338' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/pbuilderrc_Tjmm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/b1 --logfile b1/build.log mothur_1.41.21-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 9 02:47 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3338/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libreadline-dev{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 60.0 MB of archives. After unpacking 331 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libgfortran-8-dev amd64 8.3.0-6 [616 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 gfortran-8 amd64 8.3.0-6 [9375 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 gfortran amd64 4:8.3.0-1 [1432 B] Get: 47 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 ibverbs-providers amd64 22.1-1 [187 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67-dev amd64 1.67.0-13+deb10u1 [539 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-13+deb10u1 [255 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libboost-iostreams-dev amd64 1.67.0.1 [3632 B] Get: 58 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libltdl-dev amd64 2.4.6-9 [162 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libhwloc-dev amd64 1.11.12-3 [175 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libibverbs-dev amd64 22.1-1 [362 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libreadline-dev amd64 7.0-5 [133 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 60.0 MB in 1s (79.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../12-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../13-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../14-libkrb5support0_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../15-libk5crypto3_1.17-3+deb10u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../16-libssl1.1_1.1.1d-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../17-libkrb5-3_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../18-libgssapi-krb5-2_1.17-3+deb10u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../19-openssh-client_1%3a7.9p1-10+deb10u2_amd64.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../20-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../21-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../22-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../23-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../24-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../25-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../26-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../27-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../28-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../29-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../30-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../31-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../32-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../33-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../34-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../35-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../36-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../37-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../38-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../39-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../40-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../41-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../42-libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... Selecting previously unselected package libgfortran-8-dev:amd64. Preparing to unpack .../43-libgfortran-8-dev_8.3.0-6_amd64.deb ... Unpacking libgfortran-8-dev:amd64 (8.3.0-6) ... Selecting previously unselected package gfortran-8. Preparing to unpack .../44-gfortran-8_8.3.0-6_amd64.deb ... Unpacking gfortran-8 (8.3.0-6) ... Selecting previously unselected package gfortran. Preparing to unpack .../45-gfortran_4%3a8.3.0-1_amd64.deb ... Unpacking gfortran (4:8.3.0-1) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../46-libnl-3-200_3.4.0-1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../47-libnl-route-3-200_3.4.0-1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.4.0-1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../48-libibverbs1_22.1-1_amd64.deb ... Unpacking libibverbs1:amd64 (22.1-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../49-ibverbs-providers_22.1-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (22.1-1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../50-icu-devtools_63.1-6+deb10u1_amd64.deb ... Unpacking icu-devtools (63.1-6+deb10u1) ... Selecting previously unselected package libboost1.67-dev:amd64. Preparing to unpack .../51-libboost1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-regex1.67.0:amd64. Preparing to unpack .../52-libboost-regex1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../53-libicu-dev_63.1-6+deb10u1_amd64.deb ... Unpacking libicu-dev:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:amd64. Preparing to unpack .../54-libboost-regex1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:amd64. Preparing to unpack .../55-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../56-libboost-iostreams-dev_1.67.0.1_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libevent-2.1-6:amd64. Preparing to unpack .../57-libevent-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:amd64. Preparing to unpack .../58-libevent-core-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-core-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:amd64. Preparing to unpack .../59-libevent-pthreads-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-pthreads-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../60-libpsm-infinipath1_3.3+20.604758e7-6_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../61-libnuma1_2.0.12-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../62-libpsm2-2_11.2.78-1_amd64.deb ... Unpacking libpsm2-2 (11.2.78-1) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../63-librdmacm1_22.1-1_amd64.deb ... Unpacking librdmacm1:amd64 (22.1-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../64-libfabric1_1.6.2-3_amd64.deb ... Unpacking libfabric1 (1.6.2-3) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../65-libltdl7_2.4.6-9_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-9) ... Selecting previously unselected package libhwloc5:amd64. Preparing to unpack .../66-libhwloc5_1.11.12-3_amd64.deb ... Unpacking libhwloc5:amd64 (1.11.12-3) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../67-libnuma-dev_2.0.12-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.12-1) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../68-libltdl-dev_2.4.6-9_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.6-9) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../69-libhwloc-dev_1.11.12-3_amd64.deb ... Unpacking libhwloc-dev:amd64 (1.11.12-3) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../70-libpciaccess0_0.14-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.14-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../71-ocl-icd-libopencl1_2.2.12-2_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.12-2) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../72-libhwloc-plugins_1.11.12-3_amd64.deb ... Unpacking libhwloc-plugins:amd64 (1.11.12-3) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../73-libnl-3-dev_3.4.0-1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../74-libnl-route-3-dev_3.4.0-1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.4.0-1) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../75-libibverbs-dev_22.1-1_amd64.deb ... Unpacking libibverbs-dev:amd64 (22.1-1) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../76-libncurses-dev_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libpmix2:amd64. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/mothur-1.41.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.41.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/mothur-1.41.21' rm -f mothur make clean make[2]: Entering directory '/build/mothur-1.41.21' make[2]: Leaving directory '/build/mothur-1.41.21' ( cd source/uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr ) make[1]: Leaving directory '/build/mothur-1.41.21' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/mothur-1.41.21' dh_auto_build -- 64BIT_VERSION=yes make -j16 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes make[2]: Entering directory '/build/mothur-1.41.21' g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I 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source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I 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source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I 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source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engine.o source/engine.cpp source/mothur.cpp: In function 'int main(int, char**)': source/mothur.cpp:45:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system("clear"); ~~~~~~^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/currentfile.o source/currentfile.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp source/utils.cpp: In member function 'int Utils::renameFile(std::__cxx11::string, std::__cxx11::string)': source/utils.cpp:873:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ source/utils.cpp: In member function 'std::__cxx11::string Utils::sortFile(std::__cxx11::string, std::__cxx11::string)': source/utils.cpp:1105:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ source/utils.cpp: In member function 'bool Utils::mkDir(std::__cxx11::string&)': source/utils.cpp:1576:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(makeDirectoryCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I 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source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ 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source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread 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-Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%ld\n", &dmat->ntaxa); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/matrixoutputcommand.o source/commands/matrixoutputcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': source/commands/distancecommand.cpp:328:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("gzip -v " + outputFile).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::__cxx11::string)': source/commands/makefilecommand.cpp:366:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(findCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp source/venn.cpp: In member function 'std::vector > Venn::getPic(std::vector, std::vector, std::vector >)': source/venn.cpp:77:16: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without vector Venn::getPic(vector lookup, vector vCalcs, vector thisOtuLabels) { ^~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)': source/commands/clustercommand.cpp:637:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double, clusterData*)': source/commands/clustersplitcommand.cpp:1219:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergeotuscommand.o source/commands/mergeotuscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp source/commands/chimeravsearchcommand.cpp: In member function 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)': source/commands/chimeravsearchcommand.cpp:1191:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp In file included from /usr/include/string.h:494, from source/mothur.h:49, from source/commands/command.hpp:16, from source/commands/chimeravsearchcommand.h:12, from source/commands/chimeravsearchcommand.cpp:9: In function 'char* strncat(char*, const char*, size_t)', inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1141:40: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' writing 11 bytes into a region of size 9 overflows the destination [-Wstringop-overflow=] return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sharedcommand.o source/commands/sharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyrfsharedcommand.o source/commands/classifyrfsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()': source/commands/systemcommand.cpp:101:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:733:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(commandString.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:316:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("gzip -v " + outputFile).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp In file included from /usr/include/string.h:494, from source/mothur.h:49, from source/commands/command.hpp:16, from source/commands/chimerauchimecommand.h:14, from source/commands/chimerauchimecommand.cpp:10: In function 'char* strcpy(char*, const char*)', inlined from 'int driver(uchimeData*)' at source/commands/chimerauchimecommand.cpp:704:19: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:90:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' writing 6 bytes into a region of size 5 overflows the destination [-Wstringop-overflow=] return __builtin___strcpy_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)': source/datastructures/blastalign.cpp:64:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security 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-fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp source/datastructures/blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestSequences(Sequence*, int, std::vector&)': source/datastructures/blastdb.cpp:163:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blastCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ source/datastructures/blastdb.cpp: In member function 'virtual std::vector BlastDB::findClosestMegaBlast(Sequence*, int, int)': source/datastructures/blastdb.cpp:230:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blastCommand.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ source/datastructures/blastdb.cpp: In member function 'virtual void BlastDB::generateDB()': source/datastructures/blastdb.cpp:297:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/forest.o source/randomforest/forest.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)': source/read/formatcolumn.cpp:87:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(CountTable*)': source/read/formatcolumn.cpp:243:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatphylip.o source/read/formatphylip.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp g++ -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.41.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp cd source/uchime_src && ./mk && mv uchime ../../ && cd .. + CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit' + ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o' + rm -f '*.o' mk.stdout mk.stderr tmp.stderr + for CPPName in $CPPNames + echo addtargets2 addtargets2 + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 addtargets2.cpp -o addtargets2.o source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)': source/read/formatphylip.cpp:105:12: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)': source/read/formatphylip.cpp:332:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo alignchime alignchime + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchime.cpp -o alignchime.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo alignchimel alignchimel + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchimel.cpp -o alignchimel.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo alnparams alnparams + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alnparams.cpp -o alnparams.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo alpha alpha + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha.cpp -o alpha.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo alpha2 alpha2 + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha2.cpp -o alpha2.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo fractid fractid + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 fractid.cpp -o fractid.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo getparents getparents + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 getparents.cpp -o getparents.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo globalalign2 globalalign2 + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 globalalign2.cpp -o globalalign2.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo make3way make3way + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 make3way.cpp -o make3way.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo mx mx + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 mx.cpp -o mx.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo myutils myutils + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 myutils.cpp -o myutils.o + cat tmp.stderr myutils.cpp: In function 'const char* SecsToHHMMSS(int)': myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from myutils.cpp:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ myutils.cpp: In function 'const char* SecsToStr(double)': myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from myutils.cpp:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ myutils.cpp: In function 'void Progress(const char*, ...)': myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from myutils.cpp:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ myutils.cpp: In function 'void ProgressExit()': myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from myutils.cpp:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo path path + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 path.cpp -o path.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo searchchime searchchime + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 searchchime.cpp -o searchchime.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo seqdb seqdb + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 seqdb.cpp -o seqdb.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo setnucmx setnucmx + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 setnucmx.cpp -o setnucmx.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo sfasta sfasta + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 sfasta.cpp -o sfasta.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo tracebackbit tracebackbit + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 tracebackbit.cpp -o tracebackbit.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo uchime_main uchime_main + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 uchime_main.cpp -o uchime_main.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo usort usort + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 usort.cpp -o usort.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo viterbifast viterbifast + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 viterbifast.cpp -o viterbifast.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + for CPPName in $CPPNames + echo writechhit writechhit + g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/mothur-1.41.21=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread '-DVERSION="\"1.41.2\""' -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 writechhit.cpp -o writechhit.o + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + LINK_OPTS= + g++ -g -o uchime addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ + cat tmp.stderr + cat tmp.stderr + rm -f tmp.stderr + ls -lh uchime -rwxr-xr-x 1 pbuilder1 pbuilder1 13M Aug 17 11:26 uchime + sum uchime 21556 12450 g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/rarefact.o source/nast.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/collect.o source/seqnoise.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/vsearchfileparser.o source/noalign.o source/heatmapsim.o source/opticluster.o source/trialSwap2.o source/consensus.o source/nastreport.o source/fileoutput.o source/cluster.o source/refchimeratest.o source/wilcox.o source/needlemanoverlap.o source/utils.o source/sensspeccalc.o source/myseqdist.o source/subsample.o source/commandfactory.o source/heatmap.o source/weightedlinkage.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/mothur.o source/engine.o source/linearalgebra.o source/slibshuff.o source/optifitcluster.o source/dlibshuff.o source/currentfile.o source/summary.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/overlap.o source/calculators/unweighted.o source/calculators/sharedjabund.o source/calculators/chao1.o source/calculators/sharedjclass.o source/calculators/sharedsobscollectsummary.o source/calculators/gower.o source/calculators/tp.o source/calculators/prng.o source/calculators/ppv.o source/calculators/fpfn.o source/calculators/sharedjsd.o source/calculators/sharedthetan.o source/calculators/boneh.o source/calculators/uvest.o source/calculators/sharedkulczynskicody.o source/calculators/sharedsorabund.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/sharedochiai.o source/calculators/structchord.o source/calculators/accuracy.o source/calculators/fdr.o source/calculators/sharedkulczynski.o source/calculators/mcc.o source/calculators/sharedthetayc.o source/calculators/coverage.o source/calculators/sharedace.o source/calculators/sharedanderbergs.o source/calculators/sharedsobs.o source/calculators/fn.o source/calculators/parsimony.o source/calculators/sharedrjsd.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/spearman.o source/calculators/mempearson.o source/calculators/manhattan.o source/calculators/whittaker.o source/calculators/shannon.o source/calculators/sharedsorclass.o source/calculators/structeuclidean.o source/calculators/specificity.o source/calculators/sharedchao1.o source/calculators/qstat.o source/calculators/simpsoneven.o source/calculators/memchi2.o source/calculators/npshannon.o source/calculators/tn.o source/calculators/shannoneven.o source/calculators/bstick.o source/calculators/logsd.o source/calculators/solow.o source/calculators/fp.o source/calculators/sharedjest.o source/calculators/tptn.o source/calculators/odum.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedlennon.o source/calculators/structchi2.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/sharedkstest.o source/calculators/f1score.o source/calculators/sensitivity.o source/calculators/sharedmorisitahorn.o source/calculators/bergerparker.o source/calculators/npv.o source/calculators/canberra.o source/calculators/hamming.o source/calculators/shen.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/geom.o source/calculators/memeuclidean.o source/calculators/bootstrap.o source/calculators/jackknife.o source/calculators/weighted.o source/calculators/efron.o source/calculators/invsimpson.o source/calculators/sharedjackknife.o source/calculators/shannonrange.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/chimerarealigner.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/getopt_long.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/commands/clusterdoturcommand.o source/commands/distancecommand.o source/commands/mergetaxsummarycommand.o source/commands/quitcommand.o source/commands/matrixoutputcommand.o source/commands/subsamplecommand.o source/commands/removegroupscommand.o source/commands/indicatorcommand.o source/commands/chimerabellerophoncommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/getgroupscommand.o source/commands/kruskalwalliscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/classifyseqscommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/removedistscommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/createdatabasecommand.o source/commands/splitgroupscommand.o source/commands/treegroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/clustersplitcommand.o source/commands/seqerrorcommand.o source/commands/aligncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/heatmapcommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/parsefastaqcommand.o source/commands/rarefactcommand.o source/commands/mergeotuscommand.o source/commands/screenseqscommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/trimseqscommand.o source/commands/mgclustercommand.o source/commands/listseqscommand.o source/commands/makelefsecommand.o source/commands/sffmultiplecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/makecontigscommand.o source/commands/makelookupcommand.o source/commands/getcurrentcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/getcommandinfocommand.o source/commands/listotulabelscommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/removeotulabelscommand.o source/commands/chimeraperseuscommand.o source/commands/phylodiversitycommand.o source/commands/filtersharedcommand.o source/commands/anosimcommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/seqsummarycommand.o source/commands/pcacommand.o source/commands/makebiomcommand.o source/commands/metastatscommand.o source/commands/shhhercommand.o source/commands/sffinfocommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/cooccurrencecommand.o source/commands/preclustercommand.o source/commands/setdircommand.o source/commands/classifytreecommand.o source/commands/clusterfitcommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/sharedcommand.o source/commands/mergefilecommand.o source/commands/pcoacommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/getgroupcommand.o source/commands/makefastqcommand.o source/commands/helpcommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/deuniquetreecommand.o source/commands/binsequencecommand.o source/commands/getlistcountcommand.o source/commands/classifyotucommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/setseedcommand.o source/commands/homovacommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/chimeracheckcommand.o source/commands/getmimarkspackagecommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/rarefactsharedcommand.o source/commands/newcommandtemplate.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/commands/chopseqscommand.o source/commands/collectcommand.o source/commands/chimeraccodecommand.o source/commands/chimeraslayercommand.o source/commands/clearcutcommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/ordervector.o source/datastructures/optimatrix.o source/datastructures/fastamap.o source/datastructures/alignment.o source/datastructures/nameassignment.o source/datastructures/suffixtree.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/tree.o source/datastructures/kmeralign.o source/datastructures/blastalign.o source/datastructures/alignmentcell.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/rabundfloatvector.o source/datastructures/treenode.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sparsedistancematrix.o source/datastructures/oligos.o source/datastructures/counttable.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/designmap.o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedlistvector.o source/datastructures/sharedordervector.o source/datastructures/distancedb.o source/datastructures/sequenceparser.o source/datastructures/fastqread.o source/datastructures/kmer.o source/datastructures/optiblastmatrix.o source/datastructures/sparsematrix.o source/datastructures/fullmatrix.o source/datastructures/optirefmatrix.o source/datastructures/filefile.o source/datastructures/reportfile.o source/datastructures/listvector.o source/datastructures/sequencecountparser.o source/datastructures/treemap.o source/datastructures/alignmentdb.o source/datastructures/suffixdb.o source/datastructures/optidata.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/abstractdecisiontree.o source/randomforest/decisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/readblast.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readcolumn.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline make[2]: Leaving directory '/build/mothur-1.41.21' make[1]: Leaving directory '/build/mothur-1.41.21' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/mothur-1.41.21' true make[1]: Leaving directory '/build/mothur-1.41.21' dh_install dh_installdocs dh_installchangelogs dh_installman dh_installmenu dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing debian/rules override_dh_dwz make[1]: Entering directory '/build/mothur-1.41.21' echo Do not run dh_dwz due to: Do not run dh_dwz due to: echo " dwz: Too few files for multifile optimization" dwz: Too few files for multifile optimization echo " objcopy: 'debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug': No such file" objcopy: 'debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug': No such file echo " dh_dwz: objcopy --compress-debug-sections debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug returned exit code 1" dh_dwz: objcopy --compress-debug-sections debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug returned exit code 1 make[1]: Leaving directory '/build/mothur-1.41.21' dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mothur' in '../mothur_1.41.21-1_amd64.deb'. dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.41.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mothur_1.41.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3338 and its subdirectories I: Current time: Wed Aug 17 11:27:23 -12 2022 I: pbuilder-time-stamp: 1660778843 Thu Jul 15 17:04:25 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Jul 15 17:04:25 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Jul 15 17:17:26 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Jul 15 17:17:27 UTC 2021 I: mothur_1.41.21-1_amd64.changes: Format: 1.8 Date: Wed, 30 Jan 2019 11:24:42 +0100 Source: mothur Binary: mothur mothur-dbgsym Architecture: amd64 Version: 1.41.21-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mothur - sequence analysis suite for research on microbiota Changes: mothur (1.41.21-1) unstable; urgency=medium . * Do not report pre-releases * New upstream version * debhelper 12 * Standards-Version: 4.3.0 * override_dh_dwz Checksums-Sha1: 7235f56c9a9c18d67949a291ae6f3260a26641eb 147349732 mothur-dbgsym_1.41.21-1_amd64.deb 707dab8df4787f70fd010c2640d777f302fc75ad 6540 mothur_1.41.21-1_amd64.buildinfo 2a44ec6b54a8cadc5737ffa1820b3b07899f9569 4702376 mothur_1.41.21-1_amd64.deb Checksums-Sha256: 5d0d3e7e447953ffbc0021061f21862ab95d9805bd8255506a6704bdb3dab1e8 147349732 mothur-dbgsym_1.41.21-1_amd64.deb 67a09b076a86b95d5bcca5eb94f224d990be5ed2dbf3b77fa12d9f575ebc35d0 6540 mothur_1.41.21-1_amd64.buildinfo a685c19f543e7a4a1b256ba5df90703b2d674bbf2bc2cf5389f5141f9301b311 4702376 mothur_1.41.21-1_amd64.deb Files: 7c02c1bf80593de32d7008cac7aa1a96 147349732 debug optional mothur-dbgsym_1.41.21-1_amd64.deb f1f45bc80e14cfe6c3edcbe0cdfd09d6 6540 science optional mothur_1.41.21-1_amd64.buildinfo 98988541210373d63ab6f321d183f0f4 4702376 science optional mothur_1.41.21-1_amd64.deb Thu Jul 15 17:17:28 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/mothur_1.41.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/mothur_1.41.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/mothur_1.41.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/b1/mothur_1.41.21-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.B1kQKWo0UP/b2/mothur_1.41.21-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.729s) 1.729s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 1.497s) 1.497s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jul 15 17:17:32 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 15 17:17:32 UTC 2021 I: mothur from buster built successfully and reproducibly on amd64. Thu Jul 15 17:17:33 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Jul 15 17:17:33 UTC 2021 I: Submitting 8.0K b1/mothur_1.41.21-1_amd64.buildinfo.asc Thu Jul 15 17:17:35 UTC 2021 I: Submitting 8.0K b2/mothur_1.41.21-1_amd64.buildinfo.asc Thu Jul 15 17:17:37 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 15 17:17:37 UTC 2021 I: Done submitting .buildinfo files. Thu Jul 15 17:17:37 UTC 2021 I: Removing signed mothur_1.41.21-1_amd64.buildinfo.asc files: removed './b1/mothur_1.41.21-1_amd64.buildinfo.asc' removed './b2/mothur_1.41.21-1_amd64.buildinfo.asc'