mothur →
1.33.3+dfsg-1 →
armhf → 2014-03-28 09:48:07
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ mothur 1.33.3+dfsg-1 (armhf) 28 Mar 2014 06:49 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: mothur
Version: 1.33.3+dfsg-1
Source Version: 1.33.3+dfsg-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/mothur-TLq_1U/mothur-1.33.3+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/mothur-TLq_1U' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-b65e1e2d-ef17-4827-ba79-62c0bfcb43f0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7341 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8506 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'mothur' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/mothur/trunk/
Need to get 909 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main mothur 1.33.3+dfsg-1 (dsc) [2103 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main mothur 1.33.3+dfsg-1 (tar) [893 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main mothur 1.33.3+dfsg-1 (diff) [13.9 kB]
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Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-TChK0o/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 21 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libreadline-dev, gfortran, libopenmpi-dev
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libreadline-dev, gfortran, libopenmpi-dev
dpkg-deb: building package `sbuild-build-depends-mothur-dummy' in `/«BUILDDIR»/resolver-SJKE2R/apt_archive/sbuild-build-depends-mothur-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install mothur build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
adduser bsdmainutils debhelper file gettext gettext-base gfortran
gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcr0 libcroco3
libffi6 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libhwloc-dev libhwloc5
libibverbs-dev libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6
libpci-dev libpci3 libpipeline1 libreadline-dev libreadline6
libreadline6-dev libsctp1 libtinfo-dev libtorque2 libunistring0 libxml2
libxml2-dev man-db openmpi-common po-debconf zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc gfortran-doc
gfortran-4.8-doc libgfortran3-dbg groff blcr-dkms libhwloc-contrib-plugins
pkg-config less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info libhwloc-plugins lksctp-tools xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
adduser bsdmainutils debhelper file gettext gettext-base gfortran
gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcr0 libcroco3
libffi6 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libhwloc-dev libhwloc5
libibverbs-dev libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6
libpci-dev libpci3 libpipeline1 libreadline-dev libreadline6-dev libsctp1
libtinfo-dev libtorque2 libunistring0 libxml2 libxml2-dev man-db
openmpi-common po-debconf sbuild-build-depends-mothur-dummy zlib1g-dev
The following packages will be upgraded:
libreadline6
1 upgraded, 41 newly installed, 0 to remove and 20 not upgraded.
Need to get 17.0 MB/17.0 MB of archives.
After this operation, 52.8 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libreadline6 armhf 6.3-4 [122 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.6-2 [20.3 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.6-1 [961 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.17-1 [225 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libpci3 armhf 1:3.2.1-2 [53.8 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-12 [17.4 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.38.2-5 [2073 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.8.2-16 [153 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libltdl7 armhf 2.4.2-1.7 [349 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libsctp1 armhf 1.0.16+dfsg-1 [27.0 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libhwloc5 armhf 1.8.1-1 [65.0 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main adduser all 3.113+nmu3 [264 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.17-1 [55.3 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.8-dev armhf 4.8.2-16 [180 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main gfortran-4.8 armhf 4.8.2-16 [4094 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.8.2-2 [1188 B]
Get:28 http://172.17.0.1/private/ jessie-staging/main libcr0 armhf 0.8.5-2.1 [33.5 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libpci-dev armhf 1:3.2.1-2 [76.1 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140118-1 [64.8 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-4 [194 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.3-4 [1000 B]
Get:34 http://172.17.0.1/private/ jessie-staging/main libtorque2 armhf 2.4.16+dfsg-1.3 [108 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxml2-dev armhf 2.9.1+dfsg1-3 [837 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libhwloc-dev armhf 1.8.1-1 [117 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libibverbs1 armhf 1.1.7-1 [31.0 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libibverbs-dev armhf 1.1.7-1 [82.3 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libopenmpi1.6 armhf 1.6.5-8+rpi1 [1226 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main openmpi-common all 1.6.5-8+rpi1 [111 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libopenmpi-dev armhf 1.6.5-8+rpi1 [447 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.2.6-2) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up adduser (3.113+nmu3) ...
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
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Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
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Setting up libxml2-dev:armhf (2.9.1+dfsg1-3) ...
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Setting up libopenmpi-dev (1.6.5-8+rpi1) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-16 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 linux-libc-dev_3.12.6-2+rpi1
Package versions: adduser_3.113+nmu3 apt_0.9.15.4 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-2 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-1 findutils_4.4.2-7 g++_4:4.8.2-2 g++-4.8_4.8.2-16 gcc_4:4.8.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gfortran_4:4.8.2-2 gfortran-4.8_4.8.2-16 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcr0_0.8.5-2.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libffi6_3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.2-16 libgfortran3_4.8.2-16 libglib2.0-0_2.38.2-5 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libhwloc-dev_1.8.1-1 libhwloc5_1.8.1-1 libibverbs-dev_1.1.7-1 libibverbs1_1.1.7-1 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-7+b3 libltdl7_2.4.2-1.7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libopenmpi-dev_1.6.5-8+rpi1 libopenmpi1.6_1.6.5-8+rpi1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpci-dev_1:3.2.1-2 libpci3_1:3.2.1-2 libpcre3_1:8.31-2 libpipeline1_1.2.6-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline-dev_6.3-4 libreadline6_6.3-4 libreadline6-dev_6.3-4 libsctp1_1.0.16+dfsg-1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-1 libtinfo-dev_5.9+20140118-1 libtinfo5_5.9+20140118-1 libtorque2_2.4.16+dfsg-1.3 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libxml2_2.9.1+dfsg1-3 libxml2-dev_2.9.1+dfsg1-3 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.6-1 mawk_1.3.3-17 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 openmpi-common_1.6.5-8+rpi1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mothur-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 udev_204-7 util-linux_2.20.1-5.6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Mar 22 21:09:44 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./mothur_1.33.3+dfsg-1.dsc
dpkg-source: info: extracting mothur in mothur-1.33.3+dfsg
dpkg-source: info: unpacking mothur_1.33.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking mothur_1.33.3+dfsg-1.debian.tar.xz
dpkg-source: info: applying makefile.patch
dpkg-source: info: applying no_lcurses.patch
dpkg-source: info: applying drop_sse_option.patch
dpkg-source: info: applying catchall_fix.patch
dpkg-source: info: applying build_without_tty.patch
dpkg-source: info: applying uchime_link_dynamically
dpkg-source: info: applying uchime_hardening.patch
dpkg-source: info: applying spelling.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-b65e1e2d-ef17-4827-ba79-62c0bfcb43f0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package mothur
dpkg-buildpackage: source version 1.33.3+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build mothur-1.33.3+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
rm -f mothur mothur-mpi *.o mothur.*.logfile
make clean
make[2]: Entering directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
make[2]: Leaving directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
( cd uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr )
make[1]: Leaving directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
if [ 32 -eq 64 ] ; then \
dh_auto_build -- 64BIT_VERSION=yes USEMPI=yes && \
mv mothur mothur-mpi && make clean && \
dh_auto_build -- 64BIT_VERSION=yes USEMPI=no ; \
else \
dh_auto_build -- 64BIT_VERSION=no ; \
fi
make[2]: Entering directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
gfortran -c *.f
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o abstractdecisiontree.o abstractdecisiontree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o abstractrandomforest.o abstractrandomforest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o ace.o ace.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o aligncommand.o aligncommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignment.o alignment.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignmentcell.o alignmentcell.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignmentdb.o alignmentdb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o alignnode.o alignnode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o aligntree.o aligntree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o amovacommand.o amovacommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o anosimcommand.o anosimcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o averagelinkage.o averagelinkage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bayesian.o bayesian.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bellerophon.o bellerophon.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bergerparker.o bergerparker.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o binsequencecommand.o binsequencecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o blastalign.o blastalign.cpp
blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string)':
blastalign.cpp:63:30: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o blastdb.o blastdb.cpp
blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int)':
blastdb.cpp:230:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str());
^
blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
blastdb.cpp:295:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str());
^
blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
blastdb.cpp:366:34: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o boneh.o boneh.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bootstrap.o bootstrap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o bstick.o bstick.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o calcsparcc.o calcsparcc.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o calculator.o calculator.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o canberra.o canberra.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o catchallcommand.o catchallcommand.cpp
catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()':
catchallcommand.cpp:321:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
catchallcommand.cpp:384:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
catchallcommand.cpp:469:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o ccode.o ccode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chao1.o chao1.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimera.o chimera.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerabellerophoncommand.o chimerabellerophoncommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraccodecommand.o chimeraccodecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeracheckcommand.o chimeracheckcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeracheckrdp.o chimeracheckrdp.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraperseuscommand.o chimeraperseuscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerapintailcommand.o chimerapintailcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerarealigner.o chimerarealigner.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraslayer.o chimeraslayer.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimeraslayercommand.o chimeraslayercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chimerauchimecommand.o chimerauchimecommand.cpp
chimerauchimecommand.cpp: In member function 'int ChimeraUchimeCommand::driver(std::string, std::string, std::string, std::string, int&)':
chimerauchimecommand.cpp:1530:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
In file included from /usr/include/string.h:636:0,
from mothur.h:39,
from chimerauchimecommand.h:14,
from chimerauchimecommand.cpp:10:
In function 'char* strcpy(char*, const char*)',
inlined from 'int ChimeraUchimeCommand::driver(std::string, std::string, std::string, std::string, int&)' at chimerauchimecommand.cpp:1501:28:
/usr/include/arm-linux-gnueabihf/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer [enabled by default]
return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o chopseqscommand.o chopseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classify.o classify.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifyotucommand.o classifyotucommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifyrfsharedcommand.o classifyrfsharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifyseqscommand.o classifyseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifysharedcommand.o classifysharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o classifytreecommand.o classifytreecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearcut.o clearcut.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearcutcommand.o clearcutcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clearmemorycommand.o clearmemorycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cluster.o cluster.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterclassic.o clusterclassic.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clustercommand.o clustercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterdoturcommand.o clusterdoturcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clusterfragmentscommand.o clusterfragmentscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o clustersplitcommand.o clustersplitcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cmdargs.o cmdargs.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collect.o collect.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collectcommand.o collectcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o collectsharedcommand.o collectsharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o commandfactory.o commandfactory.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o commandoptionparser.o commandoptionparser.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o communitytype.o communitytype.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o completelinkage.o completelinkage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o consensusseqscommand.o consensusseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o cooccurrencecommand.o cooccurrencecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o corraxescommand.o corraxescommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o countgroupscommand.o countgroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o countseqscommand.o countseqscommand.cpp
countseqscommand.cpp: In member function 'int CountSeqsCommand::processLarge(std::string)':
countseqscommand.cpp:500:40: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
countseqscommand.cpp:502:40: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o counttable.o counttable.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o createdatabasecommand.o createdatabasecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o database.o database.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o decalc.o decalc.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o decisiontree.o decisiontree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deconvolutecommand.o deconvolutecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o degapseqscommand.o degapseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o designmap.o designmap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deuniqueseqscommand.o deuniqueseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o deuniquetreecommand.o deuniquetreecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distancecommand.o distancecommand.cpp
distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
distancecommand.cpp:516:45: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distancedb.o distancedb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o distclearcut.o distclearcut.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o dlibshuff.o dlibshuff.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o dmat.o dmat.cpp
dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
dmat.cpp:476:36: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o efron.o efron.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o engine.o engine.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fasta.o fasta.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fastamap.o fastamap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fileoutput.o fileoutput.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o filterseqscommand.o filterseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o filtersharedcommand.o filtersharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o flowdata.o flowdata.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o forest.o forest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o formatcolumn.o formatcolumn.cpp
formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)':
formatcolumn.cpp:87:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(CountTable*)':
formatcolumn.cpp:250:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o formatphylip.o formatphylip.cpp
formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
formatphylip.cpp:108:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
formatphylip.cpp:338:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o fullmatrix.o fullmatrix.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o geom.o geom.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcommandinfocommand.o getcommandinfocommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcoremicrobiomecommand.o getcoremicrobiomecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getcurrentcommand.o getcurrentcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getdistscommand.o getdistscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getgroupcommand.o getgroupcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getgroupscommand.o getgroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlabelcommand.o getlabelcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlineagecommand.o getlineagecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getlistcountcommand.o getlistcountcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getmetacommunitycommand.o getmetacommunitycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getopt_long.o getopt_long.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getotulabelscommand.o getotulabelscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getoturepcommand.o getoturepcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getotuscommand.o getotuscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getrabundcommand.o getrabundcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getrelabundcommand.o getrelabundcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getsabundcommand.o getsabundcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getseqscommand.o getseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o getsharedotucommand.o getsharedotucommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o goodscoverage.o goodscoverage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o gotohoverlap.o gotohoverlap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o gower.o gower.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o groupmap.o groupmap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hamming.o hamming.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hcluster.o hcluster.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hclustercommand.o hclustercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmap.o heatmap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapcommand.o heatmapcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapsim.o heatmapsim.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heatmapsimcommand.o heatmapsimcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o heip.o heip.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o hellinger.o hellinger.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o helpcommand.o helpcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o homovacommand.o homovacommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o indicatorcommand.o indicatorcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o inputdata.o inputdata.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o invsimpson.o invsimpson.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o jackknife.o jackknife.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmeans.o kmeans.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmer.o kmer.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmerdb.o kmerdb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmernode.o kmernode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kmertree.o kmertree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o knn.o knn.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o kruskalwalliscommand.o kruskalwalliscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o lefsecommand.o lefsecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o libshuff.o libshuff.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o libshuffcommand.o libshuffcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o linearalgebra.o linearalgebra.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listotulabelscommand.o listotulabelscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listseqscommand.o listseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o listvector.o listvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o loadlogfilecommand.o loadlogfilecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o logsd.o logsd.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makebiomcommand.o makebiomcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makecontigscommand.o makecontigscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makefastqcommand.o makefastqcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makegroupcommand.o makegroupcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makelefsecommand.o makelefsecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o makelookupcommand.o makelookupcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o maligner.o maligner.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o manhattan.o manhattan.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mantelcommand.o mantelcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o matrixoutputcommand.o matrixoutputcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memchi2.o memchi2.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memchord.o memchord.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o memeuclidean.o memeuclidean.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mempearson.o mempearson.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergefilecommand.o mergefilecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergegroupscommand.o mergegroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergesfffilecommand.o mergesfffilecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mergetaxsummarycommand.o mergetaxsummarycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o metastatscommand.o metastatscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mgclustercommand.o mgclustercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothur.o mothur.cpp
mothur.cpp: In function 'int main(int, char**)':
mothur.cpp:50:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("clear");
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurfisher.o mothurfisher.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurmetastats.o mothurmetastats.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o mothurout.o mothurout.cpp
mothurout.cpp: In member function 'int MothurOut::renameFile(std::string, std::string)':
mothurout.cpp:1258:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
mothurout.cpp:1262:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
mothurout.cpp: In member function 'std::string MothurOut::sortFile(std::string, std::string)':
mothurout.cpp:1470:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o myPerseus.o myPerseus.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o myseqdist.o myseqdist.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nameassignment.o nameassignment.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nast.o nast.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nastreport.o nastreport.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o needlemanoverlap.o needlemanoverlap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o newcommandtemplate.o newcommandtemplate.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nmdscommand.o nmdscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o noalign.o noalign.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o nocommands.o nocommands.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o normalizesharedcommand.o normalizesharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o npshannon.o npshannon.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o odum.o odum.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o optionparser.o optionparser.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o ordervector.o ordervector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o otuassociationcommand.o otuassociationcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o otuhierarchycommand.o otuhierarchycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o overlap.o overlap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pairwiseseqscommand.o pairwiseseqscommand.cpp
pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
pairwiseseqscommand.cpp:474:46: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pam.o pam.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o parsefastaqcommand.o parsefastaqcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o parselistscommand.o parselistscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o parsimony.o parsimony.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o parsimonycommand.o parsimonycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pcacommand.o pcacommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pcoacommand.o pcoacommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o phylodiversitycommand.o phylodiversitycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o phylosummary.o phylosummary.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o phylotree.o phylotree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o phylotypecommand.o phylotypecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pintail.o pintail.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o pipelinepdscommand.o pipelinepdscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o prcseqscommand.o prcseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o preclustercommand.o preclustercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o primerdesigncommand.o primerdesigncommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o prng.o prng.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o progress.o progress.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o qFinderDMM.o qFinderDMM.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o qstat.o qstat.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o qualityscores.o qualityscores.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o quitcommand.o quitcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rabundvector.o rabundvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o randomforest.o randomforest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o randomnumber.o randomnumber.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rarecalc.o rarecalc.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o raredisplay.o raredisplay.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rarefact.o rarefact.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rarefactcommand.o rarefactcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rarefactsharedcommand.o rarefactsharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readblast.o readblast.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readcluster.o readcluster.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readcolumn.o readcolumn.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readphylip.o readphylip.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readphylipvector.o readphylipvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o readtree.o readtree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o refchimeratest.o refchimeratest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o referencedb.o referencedb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o regularizeddecisiontree.o regularizeddecisiontree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o regularizedrandomforest.o regularizedrandomforest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removedistscommand.o removedistscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removegroupscommand.o removegroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removelineagecommand.o removelineagecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removeotulabelscommand.o removeotulabelscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removeotuscommand.o removeotuscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removerarecommand.o removerarecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o removeseqscommand.o removeseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o renameseqscommand.o renameseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o reportfile.o reportfile.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o reversecommand.o reversecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o rftreenode.o rftreenode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sabundvector.o sabundvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o screenseqscommand.o screenseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o secondarystructurecommand.o secondarystructurecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sensspeccommand.o sensspeccommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o seqerrorcommand.o seqerrorcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o seqnoise.o seqnoise.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o seqsummarycommand.o seqsummarycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequence.o sequence.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequencecountparser.o sequencecountparser.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequencedb.o sequencedb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sequenceparser.o sequenceparser.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o setcurrentcommand.o setcurrentcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o setdircommand.o setdircommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o setlogfilecommand.o setlogfilecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sffinfocommand.o sffinfocommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sffmultiplecommand.o sffmultiplecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shannon.o shannon.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shannoneven.o shannoneven.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shannonrange.o shannonrange.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedace.o sharedace.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedanderbergs.o sharedanderbergs.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedbraycurtis.o sharedbraycurtis.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedchao1.o sharedchao1.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedcommand.o sharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedjabund.o sharedjabund.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedjackknife.o sharedjackknife.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedjclass.o sharedjclass.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedjest.o sharedjest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedjsd.o sharedjsd.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedkstest.o sharedkstest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedkulczynski.o sharedkulczynski.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedkulczynskicody.o sharedkulczynskicody.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedlennon.o sharedlennon.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedlistvector.o sharedlistvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedmarczewski.o sharedmarczewski.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedmorisitahorn.o sharedmorisitahorn.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedochiai.o sharedochiai.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedordervector.o sharedordervector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedrabundfloatvector.o sharedrabundfloatvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedrabundvector.o sharedrabundvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedrjsd.o sharedrjsd.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsabundvector.o sharedsabundvector.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsobs.o sharedsobs.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsobscollectsummary.o sharedsobscollectsummary.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsorabund.o sharedsorabund.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsorclass.o sharedsorclass.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedsorest.o sharedsorest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedthetan.o sharedthetan.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedthetayc.o sharedthetayc.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sharedutilities.o sharedutilities.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shen.o shen.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shhhercommand.o shhhercommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o shhhseqscommand.o shhhseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o simpson.o simpson.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o simpsoneven.o simpsoneven.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o singlelinkage.o singlelinkage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o slayer.o slayer.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o slibshuff.o slibshuff.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o smithwilson.o smithwilson.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o soergel.o soergel.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o solow.o solow.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sortseqscommand.o sortseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sparcccommand.o sparcccommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sparsedistancematrix.o sparsedistancematrix.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sparsematrix.o sparsematrix.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o spearman.o spearman.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o speciesprofile.o speciesprofile.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o spline.o spline.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o splitabundcommand.o splitabundcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o splitgroupscommand.o splitgroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o splitmatrix.o splitmatrix.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o sracommand.o sracommand.cpp
sracommand.cpp:22:66: warning: trigraph ??- ignored, use -trigraphs to enable [-Wtrigraphs]
CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o structchi2.o structchi2.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o structchord.o structchord.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o structeuclidean.o structeuclidean.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o structkulczynski.o structkulczynski.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o structpearson.o structpearson.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o subsample.o subsample.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o subsamplecommand.o subsamplecommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o suffixdb.o suffixdb.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o suffixnodes.o suffixnodes.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o suffixtree.o suffixtree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o summarycommand.o summarycommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o summaryqualcommand.o summaryqualcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o summarysharedcommand.o summarysharedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o summarytaxcommand.o summarytaxcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o systemcommand.o systemcommand.cpp
systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
systemcommand.cpp:101:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o taxonomyequalizer.o taxonomyequalizer.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o taxonomynode.o taxonomynode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o tree.o tree.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treegroupscommand.o treegroupscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treemap.o treemap.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treenode.o treenode.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o treereader.o treereader.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trialSwap2.o trialSwap2.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimflowscommand.o trimflowscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimoligos.o trimoligos.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o trimseqscommand.o trimseqscommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unifracunweightedcommand.o unifracunweightedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unifracweightedcommand.o unifracweightedcommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o unweighted.o unweighted.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o uvest.o uvest.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o validcalculator.o validcalculator.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o validparameter.o validparameter.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o venn.o venn.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o venncommand.o venncommand.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o weighted.o weighted.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o weightedlinkage.o weightedlinkage.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o whittaker.o whittaker.cpp
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -I. -D_FORTIFY_SOURCE=2 -c -o wilcox.o wilcox.cpp
echo ENV_GCC_OPTS="-D_FORTIFY_SOURCE=2"
ENV_GCC_OPTS=-D_FORTIFY_SOURCE=2
echo ENV_LINK_OPTS="-Wl,-z,relro"
ENV_LINK_OPTS=-Wl,-z,relro
cd uchime_src && ENV_GCC_OPTS="-D_FORTIFY_SOURCE=2" ENV_LINK_OPTS="-Wl,-z,relro" ./mk && mv uchime .. && cd ..
addtargets2
alignchime
alignchimel
alnparams
alpha
alpha2
fractid
getparents
globalalign2
make3way
mx
myutils
path
searchchime
seqdb
setnucmx
sfasta
tracebackbit
uchime_main
usort
viterbifast
writechhit
-rwxrwxr-x 1 buildd buildd 168K Mar 28 09:45 uchime
53923 168
g++ -Wl,-z,relro -o mothur abstractdecisiontree.o abstractrandomforest.o ace.o aligncommand.o alignment.o alignmentcell.o alignmentdb.o alignnode.o aligntree.o amovacommand.o anosimcommand.o averagelinkage.o bayesian.o bellerophon.o bergerparker.o binsequencecommand.o blastalign.o blastdb.o boneh.o bootstrap.o bstick.o calcsparcc.o calculator.o canberra.o catchallcommand.o ccode.o chao1.o chimera.o chimerabellerophoncommand.o chimeraccodecommand.o chimeracheckcommand.o chimeracheckrdp.o chimeraperseuscommand.o chimerapintailcommand.o chimerarealigner.o chimeraslayer.o chimeraslayercommand.o chimerauchimecommand.o chopseqscommand.o classify.o classifyotucommand.o classifyrfsharedcommand.o classifyseqscommand.o classifysharedcommand.o classifytreecommand.o clearcut.o clearcutcommand.o clearmemorycommand.o cluster.o clusterclassic.o clustercommand.o clusterdoturcommand.o clusterfragmentscommand.o clustersplitcommand.o cmdargs.o collect.o collectcommand.o collectsharedcommand.o commandfactory.o commandoptionparser.o communitytype.o completelinkage.o consensus.o consensusseqscommand.o cooccurrencecommand.o corraxescommand.o countgroupscommand.o countseqscommand.o counttable.o coverage.o createdatabasecommand.o database.o decalc.o decisiontree.o deconvolutecommand.o degapseqscommand.o designmap.o deuniqueseqscommand.o deuniquetreecommand.o distancecommand.o distancedb.o distclearcut.o dlibshuff.o dmat.o efron.o engine.o fasta.o fastamap.o fileoutput.o filterseqscommand.o filtersharedcommand.o flowdata.o forest.o formatcolumn.o formatphylip.o fullmatrix.o geom.o getcommandinfocommand.o getcoremicrobiomecommand.o getcurrentcommand.o getdistscommand.o getgroupcommand.o getgroupscommand.o getlabelcommand.o getlineagecommand.o getlistcountcommand.o getmetacommunitycommand.o getopt_long.o getotulabelscommand.o getoturepcommand.o getotuscommand.o getrabundcommand.o getrelabundcommand.o getsabundcommand.o getseqscommand.o getsharedotucommand.o goodscoverage.o gotohoverlap.o gower.o groupmap.o hamming.o hcluster.o hclustercommand.o heatmap.o heatmapcommand.o heatmapsim.o heatmapsimcommand.o heip.o hellinger.o helpcommand.o homovacommand.o indicatorcommand.o inputdata.o invsimpson.o jackknife.o kmeans.o kmer.o kmerdb.o kmernode.o kmertree.o knn.o kruskalwalliscommand.o lefsecommand.o libshuff.o libshuffcommand.o linearalgebra.o listotulabelscommand.o listseqscommand.o listvector.o loadlogfilecommand.o logsd.o makebiomcommand.o makecontigscommand.o makefastqcommand.o makegroupcommand.o makelefsecommand.o makelookupcommand.o maligner.o manhattan.o mantelcommand.o matrixoutputcommand.o memchi2.o memchord.o memeuclidean.o mempearson.o mergefilecommand.o mergegroupscommand.o mergesfffilecommand.o mergetaxsummarycommand.o metastatscommand.o mgclustercommand.o mothur.o mothurfisher.o mothurmetastats.o mothurout.o myPerseus.o myseqdist.o nameassignment.o nast.o nastreport.o needlemanoverlap.o newcommandtemplate.o nmdscommand.o noalign.o nocommands.o normalizesharedcommand.o npshannon.o odum.o optionparser.o ordervector.o otuassociationcommand.o otuhierarchycommand.o overlap.o pairwiseseqscommand.o pam.o parsefastaqcommand.o parselistscommand.o parsimony.o parsimonycommand.o pcacommand.o pcoacommand.o phylodiversitycommand.o phylosummary.o phylotree.o phylotypecommand.o pintail.o pipelinepdscommand.o prcseqscommand.o preclustercommand.o primerdesigncommand.o prng.o progress.o qFinderDMM.o qstat.o qualityscores.o quitcommand.o rabundvector.o randomforest.o randomnumber.o rarecalc.o raredisplay.o rarefact.o rarefactcommand.o rarefactsharedcommand.o readblast.o readcluster.o readcolumn.o readphylip.o readphylipvector.o readtree.o refchimeratest.o referencedb.o regularizeddecisiontree.o regularizedrandomforest.o removedistscommand.o removegroupscommand.o removelineagecommand.o removeotulabelscommand.o removeotuscommand.o removerarecommand.o removeseqscommand.o renameseqscommand.o reportfile.o reversecommand.o rftreenode.o sabundvector.o screenseqscommand.o secondarystructurecommand.o sensspeccommand.o seqerrorcommand.o seqnoise.o seqsummarycommand.o sequence.o sequencecountparser.o sequencedb.o sequenceparser.o setcurrentcommand.o setdircommand.o setlogfilecommand.o sffinfocommand.o sffmultiplecommand.o shannon.o shannoneven.o shannonrange.o sharedace.o sharedanderbergs.o sharedbraycurtis.o sharedchao1.o sharedcommand.o sharedjabund.o sharedjackknife.o sharedjclass.o sharedjest.o sharedjsd.o sharedkstest.o sharedkulczynski.o sharedkulczynskicody.o sharedlennon.o sharedlistvector.o sharedmarczewski.o sharedmorisitahorn.o sharedochiai.o sharedordervector.o sharedrabundfloatvector.o sharedrabundvector.o sharedrjsd.o sharedsabundvector.o sharedsobs.o sharedsobscollectsummary.o sharedsorabund.o sharedsorclass.o sharedsorest.o sharedthetan.o sharedthetayc.o sharedutilities.o shen.o shhhercommand.o shhhseqscommand.o simpson.o simpsoneven.o singlelinkage.o slayer.o slibshuff.o smithwilson.o soergel.o solow.o sortseqscommand.o sparcccommand.o sparsedistancematrix.o sparsematrix.o spearman.o speciesprofile.o spline.o splitabundcommand.o splitgroupscommand.o splitmatrix.o sracommand.o structchi2.o structchord.o structeuclidean.o structkulczynski.o structpearson.o subsample.o subsamplecommand.o suffixdb.o suffixnodes.o suffixtree.o summarycommand.o summaryqualcommand.o summarysharedcommand.o summarytaxcommand.o systemcommand.o taxonomyequalizer.o taxonomynode.o tree.o treegroupscommand.o treemap.o treenode.o treereader.o trialSwap2.o trimflowscommand.o trimoligos.o trimseqscommand.o unifracunweightedcommand.o unifracweightedcommand.o unweighted.o uvest.o validcalculator.o validparameter.o venn.o venncommand.o weighted.o weightedlinkage.o whittaker.o wilcox.o bsplvb.o bsplvd.o bvalue.o daxpy.o ddot.o dpbfa.o dpbsl.o interv.o intrv.o sgram.o sinerp.o sslvrg.o stxwx.o -lreadline
strip mothur
make[2]: Leaving directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
make[1]: Leaving directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
true
make[1]: Leaving directory `/«BUILDDIR»/mothur-1.33.3+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_installmenu -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `mothur' in `../mothur_1.33.3+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mothur_1.33.3+dfsg-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build mothur-1.33.3+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140328-0947
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
mothur_1.33.3+dfsg-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Sat, 22 Mar 2014 21:33:31 +0100
Source: mothur
Binary: mothur mothur-mpi
Architecture: armhf
Version: 1.33.3+dfsg-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mothur - sequence analysis suite for research on microbiota
mothur-mpi - mpi-enabled binary for mothur
Changes:
mothur (1.33.3+dfsg-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
139585e96bc879325078d2570c57d09349e9f0af 3068744 mothur_1.33.3+dfsg-1_armhf.deb
Checksums-Sha256:
c12cc4262f3a48f9f952e78abab92daba5c6053ebd1e2a43b42118b11ae8f424 3068744 mothur_1.33.3+dfsg-1_armhf.deb
Files:
13f5ed91a577561f417e5d7898ee58da 3068744 science optional mothur_1.33.3+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
mothur_1.33.3+dfsg-1_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 3068744 bytes: control archive=1223 bytes.
823 bytes, 18 lines control
493 bytes, 8 lines md5sums
185 bytes, 7 lines * postinst #!/bin/sh
160 bytes, 5 lines * postrm #!/bin/sh
Package: mothur
Version: 1.33.3+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10983
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libreadline6 (>= 6.0), libstdc++6 (>= 4.6)
Conflicts: uchime
Provides: uchime
Section: science
Priority: optional
Homepage: http://www.mothur.org
Description: sequence analysis suite for research on microbiota
Mothur seeks to develop a single piece of open-source, expandable
software to fill the bioinformatics needs of the microbial ecology
community. It has incorporated the functionality of dotur, sons,
treeclimber, s-libshuff, unifrac, and much more. In addition to improving
the flexibility of these algorithms, a number of other features including
calculators and visualization tools were added.
drwxr-xr-x root/root 0 2014-03-28 09:46 ./
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/bin/
-rwxr-xr-x root/root 11062420 2014-03-28 09:46 ./usr/bin/mothur
-rwxr-xr-x root/root 171760 2014-03-28 09:46 ./usr/bin/uchime
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/doc/mothur/
-rw-r--r-- root/root 259 2013-09-12 08:58 ./usr/share/doc/mothur/README.Debian
-rw-r--r-- root/root 4654 2013-09-12 08:58 ./usr/share/doc/mothur/copyright
-rw-r--r-- root/root 2263 2014-03-22 20:34 ./usr/share/doc/mothur/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/man/
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/man/man1/
-rw-r--r-- root/root 568 2014-03-28 09:46 ./usr/share/man/man1/mothur.1.gz
-rw-r--r-- root/root 3395 2014-03-28 09:46 ./usr/share/man/man1/uchime.1.gz
drwxr-xr-x root/root 0 2014-03-28 09:46 ./usr/share/menu/
-rw-r--r-- root/root 176 2013-09-12 08:58 ./usr/share/menu/mothur
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 358148
Build-Time: 10391
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 225
Job: mothur_1.33.3+dfsg-1
Machine Architecture: armhf
Package: mothur
Package-Time: 10675
Source-Version: 1.33.3+dfsg-1
Space: 358148
Status: successful
Version: 1.33.3+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140328-0947
Build needed 02:57:55, 358148k disc space